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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Prolonging photoperiod promotes testosterone synthesis of Leydig cells by directly targeting local melatonin system in rooster testes

Abstract The study investigated the effects of prolonging photoperiod on the synthesis of testosterone and melatonin in roosters, and the effect of melatonin on testosterone synthesis in rooster Leydig cells as well as its molecular mechanisms. We randomly divided one hundred and twenty 20-week-old roosters into three groups and provided 6, 12.5 and 16 h light, respectively. The results showed that prolonging photoperiod promoted testosterone synthesis, decreased melatonin production, and inhibited the expression of melatonin membrane receptors MEL1A, MEL1B, MEL1C, and aralkylamine n-acetyltransferase (AANAT) in rooster testes. Subsequently, rooster Leydig cells were isolated and treated with 0, 0.1, 1, 10, and 100 ng/mL melatonin for 36 h. The results suggested that melatonin inhibited testosterone synthesis in rooster Leydig cells, and silencing MEL1A and MEL1B relieved the inhibition of melatonin on testosterone synthesis. Additionally, melatonin reduced the intracellular cyclic adenosine monophosphate (cAMP) level and the phosphorylation level of cAMP-response element binding protein (CREB), and CREB overexpression alleviated the inhibition of melatonin on testosterone synthesis. Furthermore, pretreatment with cAMP activator forskolin or protein kinase A (PKA) activator 8-bromo-cAMP blocked the inhibition of melatonin on CREB phosphorylation and testosterone synthesis. These results indicated that prolonging photoperiod promoted testosterone synthesis associated with the decrease in melatonin production and membrane receptors and biosynthetic enzyme of melatonin in rooster testes, and melatonin inhibited testosterone synthesis of rooster Leydig cells by inhibiting the cAMP/PKA/CREB pathway via MEL1A and MEL1B. This may be evidence that prolonging photoperiod could promote testosterone synthesis through the inhibition of the local melatonin pathway in rooster testes.

Xu, Gaoqing↗
DOE OSTI2023

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2024

Understanding the role of negative charge in the scaffold of an artificial enzyme for CO 2 hydrogenation on catalysis

Here, we have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [Rh I (P Et2 N gly P Et2 ) 2 ] - . Previously, we demonstrated a 2–3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Steroid responsiveness in alcohol-associated hepatitis is linked to glucocorticoid metabolism, mitochondrial repair, and heat shock proteins

Alcohol-associated hepatitis (AH) is one of the clinical presentations of alcohol-associated liver disease. AH has poor prognosis, and corticosteroids remain the mainstay of drug therapy. However, ~40% of patients do not respond to this treatment, and the mechanisms underlying the altered response to corticosteroids are not understood. The current study aimed to identify changes in hepatic protein expression associated with responsiveness to corticosteroids and prognosis in patients with AH. Patients with AH were enrolled based on the National Institute on Alcohol Abuse and Alcoholism inclusion criteria for acute AH and further confirmed by a diagnostic liver biopsy. Proteomic analysis was conducted on liver samples acquired from patients with AH grouped as nonresponders (AH-NR, n = 7) and responders (AH-R, n = 14) to corticosteroids, and nonalcohol-associated liver disease controls (n = 10). The definition of responders was based on the clinical prognostic model, the Lille Score, where a score < 0.45 classified patients as AH-R and a score > 0.45 as AH-NR. Primary outcomes used to assess steroid response were Lille Score (eg, improved liver function) and survival at 24 weeks. Reduced levels of the glucocorticoid receptor and its transcriptional co-activator, glucocorticoid modulatory element-binding protein 2, were observed in the hepatic proteome of AH-NR versus AH-R. The corticosteroid metabolizing enzyme, 11-beta-hydroxysteroid dehydrogenase 1, was increased in AH-NR versus AH-R along with elevated mitochondrial DNA repair enzymes, while several proteins of the heat shock pathway were reduced. Analysis of differentially expressed proteins in AH-NR who survived 24 weeks relative to AH-NR nonsurvivors revealed several protein expression changes, including increased levels of acute phase proteins, elevated coagulation factors, and reduced mast cell markers. This study identified hepatic proteomic changes that may predict responsiveness to corticosteroids and mortality in patients with AH.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

An overactivated ATR/CHK1 pathway is responsible for the prolonged G2 accumulation in irradiated AT cells

Induction of checkpoint responses in G1, S, and G2 phases of the cell cycle after exposure of cells to ionizing radiation (IR) is essential for maintaining genomic integrity. Ataxia telangiectasia mutated (ATM) plays a key role in initiating this response in all three phases of the cell cycle. However, cells lacking functional ATM exhibit a prolonged G2 arrest after IR, suggesting regulation by an ATM-independent checkpoint response. The mechanism for this ataxia telangiectasia (AT)-independent G2-checkpoint response remains unknown. We report here that the G2 checkpoint in irradiated human AT cells derives from an overactivation of the ATR/CHK1 pathway. Chk1 small interfering RNA abolishes the IR-induced prolonged G2 checkpoint and radiosensitizes AT cells to killing. These results link the activation of ATR/CHK1 with the prolonged G2 arrest in AT cells and show that activation of this G2 checkpoint contributes to the survival of AT cells.

NASA Discipline Radiation Health↗
DOE OSTI2026

Mechanism of Catechol Oxidation by the Coupled Bicupric Active Site of Tyrosinase: Completion of the Oxygenase/Oxidase Reaction Cycle

Tyrosinase contains a coupled binuclear copper (CBC) active site, which in its bicuprous form (deoxy-Ty) binds O 2 to form a side-on peroxide [Cu(II) 2 O 2 ] 2+ intermediate (oxy-Ty) that performs the regioselective monooxygenation of monophenols to catechols and their subsequent 2e − oxidation to quinones. Previously, we used spectroscopic, kinetic, and computational methods to elucidate the mechanism of the initial steps in the monooxygenation reaction. Herein, we investigated the final step in catecholate formation and provide experimental and computational results elucidating the catechol oxidation reaction, formally a proton-coupled 2e − process. We employed single-turnover stoppedflow absorption to observe the elusive catecholate-Cu(II) 2 OH intermediate via the anaerobic reaction of resting Cu(II) 2 OH Ty (met-Ty) with the catecholate substrate. This intermediate was cryo-trapped and characterized by electron paramagnetic resonance and X-ray absorption spectroscopies. These experimental results were correlated to quantum mechanics/molecular mechanics (QM/MM) and QM calculations to describe the complete catalytic cycle of tyrosinase, revealing that the 2e − oxidation of catechol to quinone involves two steps: (i) coupled 1H + /1e − transfer from the bound monoanionic catecholate to the bridged hydroxide of the met-Ty active site, followed by (ii) the second 1e − transfer. The latter is calculated to be the rate-limiting step in catechol oxidation, confirmed by experimental solvent kinetic isotope effect studies. Our computational data suggest that quinone release from the protein provides the necessary driving force for this reaction. These results establish a detailed description of this oxidase cycle of the tyrosinase mechanism and more broadly provide molecular-level insights into the diverse reactivity of CBC sites in biology.

QM/MM modeling↗
DOE OSTI2023

Redox Mediators in Homogeneous Co-electrocatalysis

Homogeneous electrocatalysis has been well studied over the past several decades for the conversion of small molecules to useful products for green energy applications or as chemical feedstocks. However, in order for these catalyst systems to be used in industrial applications, their activity and stability must be improved. In naturally occurring enzymes, redox equivalents (electrons, often in a concerted manner with protons) are delivered to enzyme active sites by small molecules known as redox mediators (RMs). Inspired by this, co-electrocatalytic systems with homogeneous catalysts and RMs have been developed for the conversion of alcohols, nitrogen, unsaturated organic substrates, oxygen, and carbon dioxide. In these systems, the RMs have been shown to both increase the activity of the catalyst and shift selectivity to more desired products by altering catalytic cycles and/or avoiding high-energy intermediates. However, the area is currently underdeveloped and requires additional fundamental advancements in order to become a more general strategy. Furthermore, we summarize the recent examples of homogeneous co-electrocatalysis and discuss possible future directions for the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Thermal Adaptation of Enzyme‐Mediated Processes Reduces Simulated Soil CO2 Fluxes Upon Soil Warming

Abstract Understanding factors influencing carbon effluxes from soils to the atmosphere is important in a world experiencing climatic change. Two important uncertainties related to soil organic carbon (SOC) stock responses to a changing climate are (a) whether soil microbial communities acclimate or adapt to changes in soil temperature and (b) how to represent this process in SOC models. To further explore these issues, we included thermal adaptation of enzyme‐mediated processes in a mechanistic SOC model (ReSOM) using the macromolecular rate theory. Thermal adaptation is defined here to encompass all potential responses of soil microbes and microbial communities following a change in temperature. To assess the effects of thermal adaptation of enzyme‐mediated processes on simulated SOC losses, ReSOM was applied to data collected from a 13‐year soil warming experiment. Results show that a model omitting thermal adaptation of enzyme‐mediated processes substantially overestimates observed CO 2 effluxes during the initial years of soil warming. The bias against observed CO 2 effluxes was lower for models including thermal adaptation of enzyme‐mediated processes. In addition, for a simulated linear 3°C soil warming over 100 years, models including thermal adaptation of enzyme‐mediated processes simulated SOC losses of a factor of three smaller than models omitting this process. As thermal adaptation of microbial community characteristics is generally not included in models simulating feedback between the soil, biosphere and atmosphere, we encourage future studies to assess the potential impact that microbial adaptation has on soil carbon – climate feedback representations in models. Plain Language Summary A major uncertainty in projecting how much soil organic carbon (SOC) will be converted to CO 2 as a consequence of climate change is related to how soil microbes may adapt to increasing soil temperatures. While this “microbial thermal adaptation” has been shown to occur in short‐term lab incubation experiments, its effect on SOC cycling on a decadal timescale is not clear. To address this knowledge gap, a mechanistic SOC model was used to simulate data collected from a 13‐year soil warming experiment, to assess how microbial thermal adaptation affects predicted SOC losses upon soil warming. The model results show that incorporating microbial thermal adaptation into the model led to reduced CO 2 effluxes from the soil to the atmosphere compared to the common approach of omitting this mechanism. Our results imply that projected SOC losses for the decades to come may be reduced when this mechanism is incorporated in land models. We therefore advocate for more research on the mechanisms controlling microbial thermal adaptation, and how to implement this mechanism in SOC models. Key Points A crucial aspect of soil organic carbon (SOC) models is the representation of soil microbes Predicted soil CO 2 fluxes upon soil warming are reduced when accounting for microbial thermal adaptation On a centennial time scale, this thermal adaptation results in up to a factor of three lower predicted SOC loss

Van de Broek, Marijn↗
DOE OSTI2023

One thousand soils for molecular understanding of belowground carbon cycling

While significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray computed tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Catalytic Bias of NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and its Relevance to Ethanol Production in Thermoanaerobacterium Saccharolyticum

NADH-dependent reduced ferredoxin: NADP+ oxidoreductase (Nfn) enzyme catalyzes an energy-conserving flavin-based electron bifurcation (FBEB) reaction. In microbial metabolism, Nfn links redox pools of three electron carriers - ferredoxin (Fd), NAD(H), and NADP(H) - through the following FBEB reaction: 2 NADPH + NAD+ + 2 Fdox 2 NADP+ + NADH + 2 Fdred + H+ The forward reaction is termed electron bifurcation, and the reverse reaction is electron confurcation. Catalytic bias describes an enzyme's tendency to favor one direction of a reversible reaction over the other and is expressed as the ratio of activities in the two directions. Thermoanaerobacterium saccharolyticum (Tsac) is a thermophilic, ethanologenic bacterium that ferments hemicellulose to ethanol at yields above 90%. Its Nfn enzyme is known to support ethanol production, presumably by operating in the confurcating direction to balance cellular cofactors, but this has not previously been demonstrated. To investigate the Tsac Nfn further, we heterologously expressed, purified, and reconstituted the proteins NfnS (NfnA), NfnL (NfnB), and the putative partner Fd with iron-sulfur cluster and/or FAD cofactors. Activity assays monitoring the oxidation or reduction of Fd showed that, across pH 5-10, Tsac Nfn is catalytically biased towards the confurcating direction, favoring NADPH generation over NADPH oxidation by at least fivefold. Using protein electrochemistry, we also determined the reduction potentials of the cofactors in NfnL and Fd. These results indicate that the energetic landscape of FBEB in Tsac Nfn is similar to that in an ortholog. However, Tsac Fd has redox properties distinct from previously assayed Fds, suggesting that the identity and redox properties of Fd may help determine the catalytic bias of Nfn. Additionally, we confirmed the standalone ferredoxin: NADP+ oxidoreductase (FNOR) activity of NfnL but found it to be low and likely insignificant for in vivo redox conversion. We also show how the catalytic bias of Nfn integrates with the hydrogen cycling mechanism proposed in Tsac to better explain cofactor balancing for ethanol production. Our work advances the understanding of electron transfer processes within metabolic networks for the generation of valuable bioproducts.

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

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Abstract Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

09 BIOMASS FUELS↗
DOE OSTI2024

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗
DOE OSTI2023

Stabilization of a Heme-HNO Model Complex Using a Bulky Bis-Picket Fence Porphyrin and Reactivity Studies with NO

Nitroxyl, HNO/NO – , the one-electron reduced form of NO, is suggested to take part in distinct signaling pathways in mammals and is also a key intermediate in various heme-catalyzed NO x interconversions in the nitrogen cycle. Cytochrome P450nor (Cyt P450nor) is a heme-containing enzyme that performs NO reduction to N 2 O in fungal denitrification. The reactive intermediate in this enzyme, termed “Intermediate I”, is proposed to be an Fe-NHO/Fe-NHOH type species, but it is difficult to study its electronic structure and exact protonation state due to its instability. Here, we utilize a bulky bis-picket fence porphyrin to obtain the first stable heme-HNO model complex, [Fe(3,5-Me-BAFP)(MI)(NHO)], as a model for Intermediate I, and more generally HNO adducts of heme proteins. Due to the steric hindrance of the bis-picket fence porphyrin, [Fe(3,5-Me-BAFP)(MI)(NHO)] is stable (τ 1/2 = 56 min at -30 °C), can be isolated as a solid, and is available for thorough spectroscopic characterization. In particular, we were able to solve a conundrum in the literature and provide the first full vibrational characterization of a heme-HNO complex using IR and nuclear resonance vibrational spectroscopy (NRVS). Reactivity studies of [Fe(3,5-Me-BAFP)(MI)(NHO)] with NO gas show a 91 ± 10% yield for N 2 O formation, demonstrating that heme-HNO complexes are catalytically competent intermediates for NO reduction to N 2 O in Cyt P450nor. In conclusion, the implications of these results for the mechanism of Cyt P450nor are further discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Increasing the Carbohydrate Output of Bamboo Using a Combinatorial Pretreatment

Bamboo represents a family of highly lignified biomass with significant resistance to cellulolytic enzyme degradation, and typically, a severe thermochemical pretreatment is needed to overcome its recalcitrance for producing fermentable sugars. Combinatorial pretreatments with a low holding temperature and low alkali dosage were investigated in this study in an attempt to remove the impediments to the accessibility of bamboo cellulose to enzymes and enable the efficient conversion of hemicellulose. Upon autohydrolysis at 180 °C, more than half of the hemicellulose (~58%) was solubilized, contributing to further delignification in the subsequent dilute alkali extraction (DAE). The solubilized hemicellulose mainly existed in the form of soluble xylan, which, after a novel endo-β-1,4-xylanase hydrolysis, generated a large amount of xylo-oligosaccharides with the xylobiose and xylotriose proportion reaching 72.99%. After the fractionation with combinatorial pretreatments, cellulose and xylose enzymatic hydrolysis yields were 73.36 and 86.98%, respectively, representing increments of 22.42 and 43.15% compared with the sole autohydrolysis process. Fluorescence microscopy (FM) and confocal Raman microscopy (CRM) images revealed that these dramatic improvements were caused by the deconstruction of the bamboo cell walls, including separation of the adjacent cell walls, removal of hemicellulose and lignin, migration and redistribution of lignin, and the increased exposure of cellulose. In addition, lignin chemical structure variations during the combinatorial pretreatment were analyzed with gel permeation chromatography (GPC), 2D HSQC NMR, and 31 P NMR, and the correlation between the lignin structure and enzymatic hydrolysis efficiency was investigated. In summary, this study highlighted the application of combinatorial pretreatments to maximize the carbohydrate output of bamboo and unveiled their mechanism that enabled the high-efficiency utilization of bamboo.

09 BIOMASS FUELS↗
DOE OSTI2023

Methanogens acquire and bioaccumulate nickel during reductive dissolution of nickelian pyrite

ABSTRACT Nickel (Ni) is a key component of the active site metallocofactors of numerous enzymes required for methanogenesis, including [NiFe]-hydrogenase, carbon monoxide dehydrogenase, and methyl CoM reductase, leading to a high demand for Ni among methanogens. However, methanogens often inhabit euxinic environments that favor the sequestration of nickel as metal-sulfide minerals, such as nickelian pyrite [(Ni,Fe)S 2 ], that have low solubilities and that are not considered bioavailable. Recently, however, several different model methanogens ( Methanosarcina barkeri , Methanococcus voltae , Methanococcus maripaludis ) were shown to reductively dissolve pyrite (FeS 2 ) and to utilize dissolution products to meet iron and sulfur biosynthetic demands. Here, using M. barkeri Fusaro, and laboratory-synthesized (Ni,Fe)S 2 that was physically isolated from cells using dialysis membranes, we show that trace nickel (<20 nM) abiotically solubilized from the mineral can support methanogenesis and limited growth, roughly fivefold less than the minimum concentration known to support methanogenesis. Furthermore, when provided direct contact with (Ni,Fe)S 2 , M. barkeri promoted the reductive dissolution of (Ni,Fe)S 2 and assimilated solubilized nickel, iron, and sulfur as its sole source of these elements. Cells that reductively dissolved (Ni,Fe)S 2 bioaccumulated approximately fourfold more nickel than those grown with soluble nickel and sulfide but had similar metabolic coupling efficiencies. While the mechanism for Ni uptake in archaeal methanogens is not known, homologs of the bacterial Nik uptake system were shown to be ubiquitous across methanogen genomes. Collectively, these observations indicate that (Ni,Fe)S 2 is bioavailable in anoxic environments and that methanogens can convert this mineral into nickel-, iron-, and sulfur-containing metalloenzymes to support methanogenesis and growth. IMPORTANCE Nickel is an essential metal, and its availability has changed dramatically over Earth history due to shifts in the predominant type of volcanism in the late Archean that limited its availability and an increase in euxinic conditions in the early Proterozoic that favored its precipitation as nickel sulfide minerals. Observations presented herein indicate that the methanogen, Methanosarcina barkeri , can acquire nickel at low concentration (<20 nM) from soluble and mineral sources. Furthermore, M. barkeri was shown to actively reduce nickelian pyrite; use dissolution products to meet their iron, sulfur, and nickel demands; and bioaccumulate nickel. These data help to explain how M. barkeri (and possibly other methanogens and anaerobes) can acquire nickel in contemporary and past anoxic or euxinic environments.

(NiFe)S2↗
DOE OSTI2023

The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11

SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019–2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11’s four heavy chain changes from the VH 3-53 germline sequence, $Thr^{28}_{FWRH1}$ to Ile and $Ser^{31}_{CDRH1}$ to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold

Abstract Supramolecular assemblies have gained tremendous attention due to their ability to catalyze reactions with the efficiencies of natural enzymes. Using ab initio molecular dynamics, we identify the origin of the catalysis by the supramolecular capsule Ga 4 L 6 12− on the reductive elimination reaction from gold complexes and assess their similarity to natural enzymes. By comparing the free energies of the reactants and transition states for the catalyzed and uncatalyzed reactions, we determine that an encapsulated water molecule generates electric fields that contributes the most to the reduction in the activation free energy. Although this is unlike the biomimetic scenario of catalysis through direct host-guest interactions, the electric fields from the nanocage also supports the transition state to complete the reductive elimination reaction with greater catalytic efficiency. However it is also shown that the nanocage poorly organizes the interfacial water, which in turn creates electric fields that misalign with the breaking bonds of the substrate, thus identifying new opportunities for catalytic design improvements in nanocage assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗