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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A [FeFe] Hydrogenase–Rubrerythrin Chimeric Enzyme Functions to Couple H 2 Oxidation to Reduction of H 2 O 2 in the Foodborne Pathogen Clostridium perfringens

[FeFe] hydrogenases are a diverse class of H 2 -activating enzymes with a wide range of utilities in nature. As H 2 is a promising renewable energy carrier, exploration of the increasingly realized functional diversity of [FeFe] hydrogenases is instrumental for understanding how these remarkable enzymes can benefit society and inspire new technologies. In this work, we uncover the properties of a highly unusual natural chimera composed of a [FeFe] hydrogenase and rubrerythrin as a single polypeptide. The unique combination of [FeFe] hydrogenase with rubrerythrin, an enzyme that functions in H 2 O 2 detoxification, raises the question of whether catalytic reactions, such as H 2 oxidation and H 2 O 2 reduction, are functionally linked. Herein, we express and purify a representative chimera from Clostridium perfringens (termed Cper HydR) and apply various electrochemical and spectroscopic approaches to determine its activity and confirm the presence of each of the proposed metallocofactors. The cumulative data demonstrate that the enzyme contains a surprising array of metallocofactors: the catalytic site of [FeFe] hydrogenase termed the H-cluster, two [4Fe-4S] clusters, two rubredoxin Fe(Cys) 4 centers, and a hemerythrin-like diiron site. The absence of an H 2 -evolution current in protein film voltammetry highlights an exceptional bias of this enzyme toward H 2 oxidation to the greatest extent that has been observed for a [FeFe] hydrogenase. Here, we demonstrate that Cper HydR uses H 2 , catalytically split by the hydrogenase domain, to reduce H 2 O 2 by the diiron site. Structural modeling suggests a homodimeric nature of the protein. Overall, this study demonstrates that Cper HydR is an H 2 -dependent H 2 O 2 reductase. Equipped with this information, we discuss the possible role of this enzyme as a part of the oxygen-stress response system, proposing that Cper HydR constitutes a new pathway for H 2 O 2 mitigation.

08 HYDROGEN↗
DOE OSTI2024

Evaluating Large‐Storm Dominance in High‐Resolution GCMs and Observations Across the Western Contiguous United States

Abstract Extreme precipitation events are projected to increase in frequency across much of the land‐surface as the global climate warms, but such projections have typically relied on coarse‐resolution (100–250 km) general circulation models (GCMs). The ensemble of HighResMIP GCMs presents an opportunity to evaluate how a more finely resolved atmosphere and land‐surface might enhance the fidelity of the simulated contribution of large‐magnitude storms to total precipitation, particularly across topographically complex terrain. Here, the simulation of large‐storm dominance, that is, the number of wettest days to reach half of the total annual precipitation, is quantified across the western United States (WUS) using four GCMs within the HighResMIP ensemble and their coarse resolution counterparts. Historical GCM simulations (1950–2014) are evaluated against a baseline generated from station‐observed daily precipitation (4,803 GHCN‐D stations) and from three gridded, observationally based precipitation data sets that are coarsened to match the resolution of the GCMs. All coarse‐resolution simulations produce less large‐storm dominance than in observations across the WUS. For two of the four GCMs, bias in the median large‐storm dominance is reduced in the HighResMIP simulation, decreasing by as much as 62% in the intermountain west region. However, the other GCMs show little change or even an increase (+28%) in bias of median large‐storm dominance across multiple sub‐regions. The spread in differences with resolution amongst GCMs suggests that, in addition to resolution, model structure and parameterization of precipitation generating processes also contribute to bias in simulated large‐storm dominance.

Environmental Sciences & Ecology↗
DOE OSTI2023

Microbial Models for Simulating Soil Carbon Dynamics: A Review

Abstract Soils store the largest amount of carbon (C) in the biosphere, and the C pool in soil is critical to the global C balance. Numerous microbial models have been developed over the last few decades to represent microbial processes that regulate the responses of soil organic carbon (SOC) to climate change. However, the representation of microbial processes varies, and how microbial processes are incorporated into SOC models has not been well explored. Here, we reviewed 71 microbial models to characterize the microbial processes incorporated into SOC models and analyzed variations in mechanistic complexity. We revealed that (a) four processes (microbial‐mediated decomposition, mineral interaction, microbial necromass recycling, and active and dormant microbial dynamics) are commonly incorporated in microbial models, (b) ∼48% of models simulate only one microbial process (i.e., microbial‐mediated decomposition) and 35% of models simulate two microbial processes: for example, microbial‐mediated decomposition and mineral interaction, (c) more than 80% microbial models use nonlinear equations, such as forward Michaelis‐Menten kinetics, to represent SOC decomposition, (d) the concept of persistence of SOC due to its intrinsic properties has been replaced by organo‐mineral interaction (∼39% of microbial models) that protects SOC from decomposition, and (e) various temperature and moisture modifiers and pH effects have been used to explain the environmental effect on microbial processes. In the future, to realistically incorporate microbial processes into Earth System Models, it is imperative to identify experimental evidence on rate limitation processes and firmly ground model structure on the field and laboratory data.

Environmental Sciences & Ecology↗
DOE OSTI2020

Cryo-EM structures provide insight into how E. coli F 1 F o ATP synthase accommodates symmetry mismatch

F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure and density of silicon carbide to 1.5 TPa and implications for extrasolar planets

There has been considerable recent interest in the high-pressure behavior of silicon carbide, a potential major constituent of carbon-rich exoplanets. In this work, the atomic-level structure of SiC was determined through in situ X-ray diffraction under laser-driven ramp compression up to 1.5 TPa; stresses more than seven times greater than previous static and shock data. Here we show that the B1-type structure persists over this stress range and we have constrained its equation of state (EOS). Using this data we have determined the first experimentally based mass-radius curves for a hypothetical pure SiC planet. Interior structure models are constructed for planets consisting of a SiC-rich mantle and iron-rich core. Carbide planets are found to be ~10% less dense than corresponding terrestrial planets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform

Abstract Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P) + ) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN + ). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN + (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN + with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA + ), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P) + .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2021

Comparison of short-range order in irradiated dysprosium titanates

Abstract The structural response of Dy 2 TiO 5 oxide under swift heavy ion irradiation (2.2 GeV Au ions) was studied over a range of structural length scales utilizing neutron total scattering experiments. Refinement of diffraction data confirms that the long-range orthorhombic structure is susceptible to ion beam-induced amorphization with limited crystalline fraction remaining after irradiation to 8 × 10 12 ions/cm 2 . In contrast, the local atomic arrangement, examined through pair distribution function analysis, shows only subtle changes after irradiation and is still described best by the original orthorhombic structural model. A comparison to Dy 2 Ti 2 O 7 pyrochlore oxide under the same irradiation conditions reveals a different behavior: while the dysprosium titanate pyrochlore is more radiation resistant over the long-range with smaller degree of amorphization as compared to Dy 2 TiO 5 , the former involves more local atomic rearrangements, best described by a pyrochlore-to-weberite-type transformation. These results highlight the importance of short-range and medium-range order analysis for a comprehensive description of radiation behavior.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

De novo design of high-affinity binders of bioactive helical peptides

Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity to structured proteins. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A novel bacterial protein family that catalyses nitrous oxide reduction

Nitrous oxide (N 2 O), a driver of global warming and climate change, has reached unprecedented concentrations in Earth’s atmosphere. Current N 2 O sources outpace N 2 O sinks, emphasizing the need for comprehensive understanding of processes that consume N 2 O. Microbes that express the enzyme N 2 O reductase (N 2 OR) convert N 2 O to climate change-neutral dinitrogen (N 2 ). Known N 2 ORs belong to the canonical clade I and clade II NosZ reductases and are considered key enzymes for N 2 O reduction. Here we report a previously unrecognized protein family with a role in N 2 O reduction, clade III lactonase-type N 2 OR (L-N 2 OR), which diverges in sequence from canonical NosZ but conserves three-dimensional protein structural features. Integrated physiological, metagenomic, proteomic and structural modelling studies demonstrate that L-N 2 ORs catalyse N 2 O reduction. L-N 2 OR genes occur in several phyla, predominantly in uncultured taxa with broad geographic distribution. Our findings expand the known diversity of N 2 ORs and implicate previously unrecognized taxa (for example, Nitrospinota) in N 2 O consumption. In conclusion, the expansion of N 2 OR diversity and the identification of a novel type of catalyst for N 2 O reduction advances the understanding of N 2 O sinks, has implications for greenhouse gas emission and climate change modelling, and expands opportunities for innovative biotechnologies aimed at curbing N 2 O emissions.

He, Guang 何广 [Univ. of Tennessee, Knoxville, TN (U↗
DOE OSTI2025

NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor NUB1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system with human components and revealed that NUB1 uses the intrinsic instability of FAT10 to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin-independent and p97-independent manner. Using hydrogen–deuterium exchange, structural modeling and site-directed mutagenesis, we identified the formation of an intricate complex with FAT10 that activates NUB1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic NUB1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These findings identified a previously unknown mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.

Arkinson, Connor↗
DOE OSTI2023

Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes

X-ray absorption spectroscopy (XAS) is a premier technique for materials characterization, providing key information about the local chemical environment of the absorber atom. In this work, we develop a database of sulfur K-edge XAS spectra of crystalline and amorphous lithium thiophosphate materials based on the atomic structures reported in Chem. Mater., 34, 6702 (2022). The XAS database is based on simulations using the excited electron and core-hole pseudopotential approach implemented in the Vienna Ab initio Simulation Package. Our database contains 2681 S K-edge XAS spectra for 66 crystalline and glassy structure models, making it the largest collection of first-principles computational XAS spectra for glass/ceramic lithium thiophosphates to date. This database can be used to correlate S spectral features with distinct S species based on their local coordination and short-range ordering in sulfide-based solid electrolytes. The data is openly distributed via the Materials Cloud, allowing researchers to access it for free and use it for further analysis, such as spectral fingerprinting, matching with experiments, and developing machine learning models.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Unlocking soybean meal pectin recalcitrance using a multi-enzyme cocktail approach

Pectin is a complex plant heteropolysaccharide whose structure and function differ depending on its source. In animal feed, breaking down pectin is essential, as its presence increases feed viscosity and reduces nutrient absorption. Soybean meal, a protein-rich poultry feed ingredient, contains significant amounts of pectin, the structure of which remains unclear. Consequently, the enzyme activities required to degrade soybean meal pectin and how they interact are still open questions. In this study, we produced 15 recombinant fungal carbohydrate-active enzymes (CAZymes) identified from fungal secretomes acting on pectin. After observing that these enzymes were not active on soybean meal pectin when used alone, we developed a semi-miniaturized method to evaluate their effect as multi-activity cocktails. We designed and tested 12 enzyme pools, containing up to 15 different CAZymes, using several hydrolysis markers. Thanks to our multiactivity enzymatic approach combined with a Pearson correlation matrix, we identified 10 fungal CAZymes efficient on soybean meal pectin, 9 of which originate from Talaromyces versatilis. Based on enzyme specificity and linkage analysis, we propose a structural model for soybean meal pectin. Our findings underscore the importance of combining CAZymes to improve the degradation of agricultural co-products.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Fatty acid capped, metal oxo clusters as the smallest conceivable nanocrystal prototypes

Metal oxo clusters of the type M 6 O 4 (OH) 4 (OOCR) 12 (M = Zr or Hf) are valuable building blocks for materials science. Here, we synthesize a series of zirconium and hafnium oxo clusters with ligands that are typically used to stabilize oxide nanocrystals (fatty acids with long and/or branched chains). The fatty acid capped oxo clusters have a high solubility but do not crystallize, precluding traditional purification and single-crystal XRD analysis. We thus develop alternative purification strategies and we use X-ray total scattering and Pair Distribution Function (PDF) analysis as our main method to elucidate the structure of the cluster core. We identify the correct structure from a series of possible clusters (Zr3, Zr4, Zr6, Zr12, Zr10, and Zr26). Excellent refinements are only obtained when the ligands are part of the structure model. Further evidence for the cluster composition is provided by nuclear magnetic resonance (NMR), infrared spectroscopy (FTIR), thermogravimetry analysis (TGA), and mass spectrometry (MS). We find that hydrogen bonded carboxylic acid is an intrinsic part of the oxo cluster. Using our analytical tools, we elucidate the conversion from a Zr6 monomer to a Zr12 dimer (and vice versa), induced by carboxylate ligand exchange. Finally, we compare the catalytic performance of Zr12-oleate clusters with oleate capped, 5.5 nm zirconium oxide nanocrystals in the esterification of oleic acid with ethanol. The oxo clusters present a five times higher reaction rate, due to their higher surface area. Since the oxo clusters are the lower limit of downscaling oxide nanocrystals, we present them as appealing catalytic materials, and as atomically precise model systems. In addition, the lessons learned regarding PDF analysis are applicable to other areas of cluster science as well, from semiconductor and metal clusters, to polyoxometalates.

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

Effect of rare earth size on network structure and glass forming ability in binary aluminum garnets

Rare earth aluminate glasses are potentially useful for optical, luminescence, and laser applications. As reluctant glass formers, these materials exhibit unconventional atomic structures. To better understand how their structures correlate with glass formation, we investigate two rare earth aluminum garnet melts, La 3 Al 5 O 12 (LAG) and Yb 3 Al 5 O 12 (YbAG), which represent the relative extremes of good and poor glass forming ability in rare earth aluminates. Structural models have been refined to high-energy X-ray diffraction data over 1340–2740 K. Both melts contain mixtures of AlO 4 , AlO 5 , and AlO 6 polyhedra, with larger fractions of [5] Al and [6] Al in YbAG. Extrapolation of the Al–O coordination distributions to the glass transition match closely with 27 Al nuclear magnetic resonance measurements of (La 1−z Y z ) 3 Al 5 O 12 glasses, z = 0 to 1. During cooling, the mean coordination numbers increase for La–O in LAG from 6.45(8) to 6.98(8) and for Yb–O in YbAG from 6.02(8) to 6.21(8). Linkedness among Al–O polyhedra at ∼2450 K is mostly corner-sharing, with 9% edge-sharing in LAG and 19% in YbAG. Among [4] Al units, both melts have 6% edge-sharing that convert to all corner-sharing upon cooling. Network connectivity is compared using a newly defined metric, K n , that is similar to the Q n distribution but that accounts for the edge-sharing and triply bonded oxygen present in these melts. The lower glass forming ability in YbAG as compared to LAG correlates with more edge-sharing, associated with the larger fractions of [5] Al and [6] Al, and lower connectivity among [4] Al units.

Wilke, Stephen K. [Materials Development, Inc., Ar↗
DOE OSTI2020

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC–MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗