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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals

The main protease of SARS-CoV-2 (M pro ) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in M pro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 M pro mutants provided structural insight into their altered functionality. Additionally, we show M pro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting M pro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Zeolitic Imidazole Framework Decorated Substrates for Lead Removal From Water

Lead contamination in water supplies necessitates efficient and mechanistically understood removal strategies. Zeolitic imidazole frameworks (ZIFs) are promising adsorbents; however, ZIF-67 (Co-based) is more susceptible to hydrolysis than its zinc analogue ZIF-8, raising questions about stability during metal uptake. In this study, we systematically compare ZIF-8 and ZIF-67 under controlled pH conditions and evaluate how substrate anchoring influences hydrolytic stability and Pb 2+ adsorption behavior. By integrating adsorption capacity measurements, kinetic analysis, metal-node leaching data, and structural characterization, we distinguish ion exchange from framework degradation and clarify the temporal interplay between adsorption and hydrolysis. Although ZIF-67 exhibits greater hydrolytic sensitivity, coordination with phosphoryl-bearing Mucor hiemalis membranes significantly reduces Co 2+ leaching and enhances structural retention. Under the optimized conditions (pH 5), ZIF-67@Mucor achieves a maximum Pb 2+ adsorption capacity of 867 mg g −1 . These findings demonstrate that substrate-dependent stabilization enables controlled exploitation of ZIF reactivity for aqueous metal remediation.

Adsorption↗
DOE OSTI2013

Uniform, Homogenous Coatings of Carbon Nanohorns on Arbitrary Substrates from Common Solvents

ABSTRACT: We demonstrate a facile technique to electro- phoretically deposit homogenous assemblies of single-walled carbon nanohorns (CNHs) from common solvents such as acetone and water onto nearly any substrate including insulators, dielectrics, and three-dimensional metal foams, in many cases without the aid of surfactants. This enables the generation of pristine film-coatings formed on time scales as short as a few seconds and on three-dimensional templates that enable the formation of freestanding polymer-CNH supported materials. As electrophoretic deposition is usually only practical on conductive electrodes, we emphasize our observation of efficient deposition on nearly any material, including nonconductive substrates. The one-step versatility of deposition on these materials provides the capability to directly assemble CNH materials onto functional surfaces for a broad range of applications. In this manner, we utilized as-deposited CNH films as conductometric gas sensors exhibiting better sensitivity in comparison to equivalent single-walled carbon nanotube sensors. This gives a route toward scalable and inexpensive solution-based processing routes to manufacture functional nanocarbon materials for catalysis, energy, and sensing applications, among others.

Oakes, Landon↗
DOE OSTI2014

Characterization of a Cross-Linked Protein-Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13 C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13 C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process

Silakov, Alexey↗
DOE OSTI2021

Nickel–Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F 430 . The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C–S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni–thiol interaction between Ni(II)–MCR and inhibitor CoMSH, a Ni(I)–thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)–disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)–sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)–N/O complex, not Ni(I)–S. These studies rule out direct Ni(I)–sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)–sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗
DOE OSTI2019

Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The “Undoing” of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network

Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen–deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein–solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Lastly, using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

MoS 2 –OH Bilayer-Mediated Growth of Inch-Sized Monolayer MoS 2 on Arbitrary Substrates

Due to remarkable electronic property, optical transparency, and mechanical flexibility, monolayer molybdenum disulfide (MoS 2 ) has been demonstrated to be promising for electronic and optoelectronic devices. To date, the growth of high-quality and large-scale monolayer MoS 2 has been one of the main challenges for practical applications. In this paper, we present a MoS 2 –OH bilayer-mediated method that can fabricate inch-sized monolayer MoS 2 on arbitrary substrates. This approach relies on a layer of hydroxide groups (-OH) that are preferentially attached to the (001) surface of MoS 2 to form a MoS 2 –OH bilayer structure for growth of large-area monolayer MoS 2 during the growth process. Specifically, the hydroxide layer impedes vertical growth of MoS 2 layers along the [001] zone axis, promoting the monolayer growth of MoS 2 , constrains growth of the MoS 2 monolayer only in the lateral direction into larger area, and effectively reduces sulfur vacancies and defects according to density functional theory calculations. Finally, the hydroxide groups advantageously prevent the MoS 2 from interface oxidation in air, rendering high-quality MoS 2 monolayers with carrier mobility up to ~30 cm 2 V –1 s –1 . Using this approach, inch-sized uniform monolayer MoS 2 has been fabricated on the sapphire and mica and high-quality monolayer MoS 2 of single-crystalline domains exceeding 200 μm has been grown on various substrates including amorphous SiO 2 and quartz and crystalline Si, SiC, Si 3 N 4 , and graphene Finally, this method provides a new opportunity for the monolayer growth of other two-dimensional transition metal dichalcogenides such as WS 2 and MoSe 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2019

Substrate-Triggered Formation of a Peroxo-Fe 2 (III/III) Intermediate during Fatty Acid Decarboxylation by UndA

The iron-dependent oxidase UndA cleaves one C3–H bond and the C1–C2 bond of dodecanoic acid to produce 1-undecene and CO 2 . A published X-ray crystal structure showed that UndA has a heme-oxygenase-like fold, thus associating it with a structural superfamily that includes known and postulated non-heme diiron proteins, but revealed only a single iron ion in the active site. Mechanisms proposed for initiation of decarboxylation by cleavage of the C3–H bond using a monoiron cofactor to activate O 2 necessarily invoked unusual or potentially unfeasible steps. Here we present spectroscopic, crystallographic, and biochemical evidence that the cofactor of Pseudomonas fluorescens Pf-5 UndA is actually a diiron cluster and show that binding of the substrate triggers rapid addition of O 2 to the Fe 2 (II/II) cofactor to produce a transient peroxo-Fe 2 (III/III) intermediate. Finally, the observations of a diiron cofactor and substrate-triggered formation of a peroxo-Fe 2 (III/III) intermediate suggest a small set of possible mechanisms for O 2 , C3–H and C1–C2 activation by UndA; these routes obviate the problematic steps of the earlier hypotheses that invoked a single iron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

The Origin of Surface-Enhanced Raman Scattering of 4,4' -Biphenyldicarboxylate on Silver Substrates

We combine scanning electron microscopy, atomic force microscopy, surface-enhanced Raman scattering (SERS), and tools of computational chemistry to investigate the origin of Raman scattering of 4,4’-biphenyldicarboxylic acid adsorbed as 4,4’-biphenyldicarboxylate on two different silver substrates. The first consists of a 100 nm deep cylindrical aperture embedded in an array of cylindrical nano-holes featuring an average diameter of 350 nm and a periodicity of 700 nm. The second is a nano-junction formed by a 100 nm silver nano-particle coated with the adsorbate and a flat silver surface. We find that the underlying background signal in the SERS spectra collected from the former strongly resemble the SERS spectra of the nano-sphere-featuring substrate, engineered to operate in the charge transfer plasmon limit. Our analysis of a series of SERS spectra consecutively collected from one nano-cylinder suggests that the optical response of a single molecule can be extracted, its brightest Raman active mode enhanced by a factor of 7.4 x 106.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Electronic and Vibrational Properties of meso -Tetraphenylporphyrin on Silver Substrates

The electronic and vibrational properties of meso-tetraphenylporphyrin (mtpp) on silver substrates are investigated using UV–vis and surface-enhanced resonance Raman scattering (SERRS) spectroscopy. Whereas the vibrational signatures associated with the tetrapyrrole backbone exhibit minor variations throughout sequences of consecutively recorded SERRS spectra, the C = C stretching vibrational modes localized on the meso-phenyl moieties of mtpp exhibit noticeable intensity fluctuations, masked in the average SERRS response. Finally, we attribute the observed vibrational-state-specific blinking events to conformational changes in mtpp, namely, torsional flexibility which mediates the coupling between the π-framework of the meso-phenyls and the underlying metal substrate.

El-Khoury, Patrick Z.↗
DOE OSTI2017

Stabilization of ultrathin (hydroxy)oxide films on transition metal substrates for electrochemical energy conversion

Design of cost-effective electrocatalysts with enhanced stability and activity is of paramount importance for the next generation of energy conversion systems, including fuel cells and electrolyzers. However, electrocatalytic materials generally improve one of these properties at the expense of the other. Here, using Density Functional Theory calculations and electrochemical surface science measurements, we explore atomic-level features of ultrathin (hydroxy)oxide films on transition metal substrates and demonstrate that these films exhibit both excellent stability and activity for electrocatalytic applications. The films adopt structures with stabilities that significantly exceed bulk Pourbaix limits, including stoichiometries not found in bulk and properties that are tunable by controlling voltage, film composition, and substrate identity. Using nickel (hydroxy)oxide/Pt(111) as an example, we further show how the films enhance activity for hydrogen evolution through a bifunctional effect. Finally, the results suggest design principles for a new class of electrocatalysts with simultaneously enhanced stability and activity for energy conversion.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Computational approaches to substrate-based cell motility

Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realization of active, self-propelled ‘particles’, a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity, and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recently in its modeling on the whole cell level. Furthermore we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organized systems such as living cells.

25 ENERGY STORAGE↗
DOE OSTI2018

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

Abstract Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A partially-open inward-facing intermediate conformation of LeuT is associated with Na + release and substrate transport

Here, neurotransmitter:sodium symporters (NSS), targets of antidepressants and psychostimulants, clear neurotransmitters from the synaptic cleft through sodium (Na + )-coupled transport. Substrate and Na + are thought to be transported from the extracellular to intracellular space through an alternating access mechanism by coordinated conformational rearrangements in the symporter that alternately expose the binding sites to each side of the membrane. However, the mechanism by which the binding of ligands coordinates conformational changes occurring on opposite sides of the membrane is not well understood. Here, we report the use of single-molecule fluorescence resonance energy transfer (smFRET) techniques to image transitions between distinct conformational states on both the extracellular and intracellular sides of the prokaryotic NSS LeuT, including partially open intermediates associated with transport activity. The nature and functional context of these hitherto unidentified intermediate states shed new light on the allosteric mechanism that couples substrate and Na + symport by the NSS family through conformational dynamics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis

The conserved decapping enzyme Dcp2 recognizes and removes the 5' eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K . lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis.

Science & Technology - Other Topics↗