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Results for “oligomerization”

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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems1. In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP–AMP synthase–stimulator of interferon genes (cGAS–STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response2, 3–4. Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.

Doherty, Erin E↗
DOE OSTI2021

Molecular organization of the E. coli cellulose synthase macrocomplex

Cellulose is frequently found in communities of sessile bacteria called biofilms. Escherichia coli and other enterobacteriaceae modify cellulose with phosphoethanolamine (pEtN) to promote host tissue adhesion. The E. coli pEtN cellulose biosynthesis machinery contains the catalytic BcsA–B complex that synthesizes and secretes cellulose, in addition to five other subunits. The membrane-anchored periplasmic BcsG subunit catalyzes pEtN modification. Here we present the structure of the roughly 1 MDa E. coli Bcs complex, consisting of one BcsA enzyme associated with six copies of BcsB, determined by single-particle cryo-electron microscopy. BcsB homo-oligomerizes primarily through interactions between its carbohydrate-binding domains as well as intermolecular beta-sheet formation. The BcsB hexamer creates a half spiral whose open side accommodates two BcsG subunits, directly adjacent to BcsA’s periplasmic channel exit. The cytosolic BcsE and BcsQ subunits associate with BcsA’s regulatory PilZ domain. As a result, the macrocomplex is a fascinating example of cellulose synthase specification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP

Abstract The Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production

GRB2 is an adaptor protein required for facilitating cytoplasmic signaling complexes from a wide array of binding partners. GRB2 has been reported to exist in either a monomeric or dimeric state in crystal and solution. GRB2 dimers are formed by the exchange of protein segments between domains, otherwise known as “domain-swapping”. Swapping has been described between SH2 and C-terminal SH3 domains in the full-length structure of GRB2 (SH2/C–SH3 domain-swapped dimer), as well as between α-helixes in isolated GRB2 SH2 domains (SH2/SH2 domain-swapped dimer). Interestingly, SH2/SH2 domain-swapping has not been observed within the full-length protein, nor have the functional influences of this novel oligomeric conformation been explored. We herein generated a model of full-length GRB2 dimer with an SH2/SH2 domain-swapped conformation supported by in-line SEC–MALS–SAXS analyses. This conformation is consistent with the previously reported truncated GRB2 SH2/SH2 domain-swapped dimer but different from the previously reported, full-length SH2/C-terminal SH3 (C–SH3) domain-swapped dimer. Our model is also validated by several novel full-length GRB2 mutants that favor either a monomeric or a dimeric state through mutations within the SH2 domain that abrogate or promote SH2/SH2 domain-swapping. GRB2 knockdown and re-expression of selected monomeric and dimeric mutants in a T cell lymphoma cell line led to notable defects in clustering of the adaptor protein LAT and IL-2 release in response to TCR stimulation. These results mirrored similarly-impaired IL-2 release in GRB2-deficient cells. These studies show that a novel dimeric GRB2 conformation with domain-swapping between SH2 domains and monomer/dimer transitions are critical for GRB2 to facilitate early signaling complexes in human T cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dynamics and activation of membrane-bound B cell receptor assembly

B-cell receptor (BCR) complexes are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes have been published that validates the asymmetric organization of the BCR complex. Here, we carry out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identify two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding causes increased flexibility in regions distal to the antigen binding site. Second, antigen binding alters the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements lead to changes in localized lipid composition. Our work indirectly supports the conformational-change induced models of BCR activation and contributes to the understanding of the antigen-dependent activation mechanism of BCRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

From cellulose to 1,2,4-benzenetriol via catalytic degradation over a wood-based activated carbon catalyst

In this study, spherical P-doped activated carbon (CSP) was obtained from poplar bark by microwave carbonization with phosphoric acid as the dopant and activating agent. Phosphorus bonded with four oxygen atoms to form a phosphate-like structure rather than directly bonding with C atoms in CSP; such groups can provide Lewis acid active sites with moderately strong acidity. The Lewis acid and total acid content increased with increasing phosphoric acid doping ratio. The use of phosphoric acid as an activating agent promotes the formation of a developed porous structure. CSP 1 (mass ratio of raw material to acid = 1 : 1) had a specific surface area of 1115 m 2 g –1 with developed micro–mesoporous structures, mainly micropores. Investigation of the activity of CSP in catalytic cellulose hydrolysis during hydrothermal degradation showed that Brønsted acid sites promote hydrolysis and dehydration of cellulose, Lewis acid sites promote subsequent reactions such as isomerization, rearrangement, and oligomerization, and the developed pores can provide reaction sites and facilitate reactant transportation. The optimal reaction conditions, i.e. , 1 h at 230 °C and 1 MPa with CSP 1 (0.4 g) as the catalyst, gave a cellulose conversion of >99.9%, with 42.30% selectivity for 1,2,4-benzenetriol. This study provides an effective method for preparing 1,2,4-benzenetriol from cellulose with biomass-based activated carbon as the catalyst, which enables green synthesis of 1,2,4-benzenetriol and promotes the use of biomass waste resources.

1,2,4-benzenetriol↗
DOE OSTI2020

Production of renewable alcohols from maple wood using supercritical methanol hydrodeoxygenation in a semi-continuous flowthrough reactor

Biomass conversion to alcohols using supercritical methanol depolymerization and hydrodeoxygenation (SCM-DHO) with CuMgAl mixed metal oxide is a promising process for biofuel production. Here, we demonstrate how maple wood can be converted at high weight loadings and product concentrations in a batch and a semi-continuous reactor to a mixture of C 2 –C 10 linear and cyclic alcohols. Maple wood was solubilized semi-continuously in supercritical methanol and then converted to a mixture of C 2 –C 9 alcohols and aromatics over a packed bed of CuMgAlO x catalyst. Up to 95 wt% of maple wood can be solubilized in the methanol by using four temperature holds at 190, 230, 300, and 330 °C. Lignin was solubilized at 190 and 230 °C to a mixture of monomers, dimers, and trimers while hemicellulose and cellulose solubilized at 300 and 330 °C to a mixture of oligomeric sugars and liquefaction products. The hemicellulose, cellulose, and lignin were converted to C 2 –C 10 alcohol fuel precursors over a packed bed of CuMgAlO x catalyst with 70–80% carbon yield of the entire maple wood. The methanol reforming activity of the catalyst decreased by 25% over four beds of biomass, which corresponds to 5 turnovers for the catalyst, but was regenerable after calcination and reduction. In batch reactions, maple wood was converted at 10 wt% in methanol with 93% carbon yield to liquid products. The product concentration can be increased to 20 wt% by partially replacing the methanol with liquid products. The yield of alcohols in the semi-continuous reactor was approximately 30% lower than in batch reactions likely due to degradation of lignin and cellulose during solubilization. These results show that solubilization of whole biomass can be separated from catalytic conversion of the intermediates while still achieving a high yield of products. However, close contact of the catalyst and the biomass during solubilization is critical to achieve the highest yields and concentration of products.

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

Effects of nanoconfinement and surface charge on iron adsorption on mesoporous silica

Here, we present a combined molecular dynamics (MD) simulation and X-ray absorption fine structure (XAFS) spectroscopic investigation of aqueous iron adsorption on nanoconfined amorphous silica surfaces. The simulation models examine the effects of pore size, pH (surface charge), iron valency, and counter-ion (chloride or hydroxide). The simulation methods were validated by comparing the coordination environment of adsorbed iron with coordination numbers and bond lengths derived from XAFS. In the MD models, nanoconfinement effects on local iron coordination were investigated by comparing results for unconfined silica surfaces and in confined domains within 2 nm, 4 nm, and 8 nm pores. Experimentally, coordination environments of iron adsorbed onto mesoporous silica with 4 nm and 8 nm pores at pH 7.5 were investigated. The effect of pH in the MD models was included by simulating Fe(II) adsorption onto negatively charged SiO 2 surfaces and Fe(III) adsorption on neutral surfaces. The simulation results show that iron adsorption depends significantly on silica surface charge, as expected based on electrostatic interactions. Adsorption on a negatively charged surface is an order of magnitude greater than on the neutral surface, and simulated surface coverages are consistent with experimental results. Pore size effects from the MD simulations were most notable in the adsorption of Fe(II) at deprotonated surface sites (SiO - ), but adsorption trends varied with concentration and aqueous Fe speciation. The coordination environment of adsorbed iron varied significantly with the type of anion. Considerable ion pairing with hydroxide anions led to the formation of oligomeric surface complexes and aqueous species, resulting in larger iron hydroxide clusters at higher surface loadings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Effect of metallosupramolecular polymer concentration on the synthesis of poly[n]catenanes

Poly[n]catenanes are a class of polymers that are composed entirely of interlocked rings. One synthetic route to these polymers involves the formation of a metallosupramolecular polymer (MSP) that consists of alternating units of macrocyclic and linear thread components. Ring closure of the thread components has been shown to yield a mixture of cyclic, linear, and branched poly[n]catenanes. Reported herein are investigations into this synthetic methodology, with a focus on a more detailed understanding of the crude product distribution and investigations into how the concentration of the MSP during the ring closing reaction impacts the resulting poly[n]catenanes. In addition to a better understanding of the molecular products obtained in these reactions, the results show that the concentration of the reaction can be used to tune the size and type of poly[n]catenanes accessed. At low concentrations the interlocked product distribution is limited to primarily oligomeric and small cyclic catenanes (number average molar mass $\overline{Mn}$ = 6.2 kg mol -1 , number of rings = 4). However, the same reaction at increased concentration can yield branched poly[n]catenanes with an $\overline{Mn}$ ca. 21 kg mol -1 and evidence of structures with as many as 640 interlocked rings (1000 kg mol -1 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Development of an ammonia pretreatment that creates synergies between biorefineries and advanced biomass logistics models

In this study, a novel ammonia-based pretreatment for densified lignocellulosic biomass was developed to reduce ammonia usage and integrate with viable biomass logistics scenarios. The COmpacted Biomass with Recycled Ammonia (COBRA) pretreatment performed at 100 °C allows >95% conversion of sugarcane bagasse (SCB) carbohydrates into soluble monomeric and oligomeric sugars (glucose and xylose) using industrially relevant 6% glucan loading (~21% solids loading) enzymatic hydrolysis conditions at reduced enzyme loadings. Pretreatment via COBRA with simultaneous lignin extraction (COBRA-LE) improved Saccharomyces cerevisiae 424A(LNH-ST) metabolic yield from 89% to 97.5% relative to COBRA without delignification, allowing a process ethanol yield of 71.6%. A technoeconomic analysis on SCB biorefining to ethanol in the state of São Paulo, Brazil, compared COBRA to other mature technologies, such as AFEX and steam-explosion. Amongst all scenarios studied, biorefineries based on COBRA-LE pretreatment offered the lowest average minimum ethanol selling price of US$1.45 per gallon ethanol. COBRA pretreatment was subsequently tested on perennial grasses and hardwoods, and >80% total sugar yields were achieved for all cases.

09 BIOMASS FUELS↗
DOE OSTI2024

Tracking the reaction networks of acetaldehyde oxide and glyoxal oxide Criegee intermediates in the ozone-assisted oxidation reaction of crotonaldehyde

The reaction of unsaturated compounds with ozone (O 3 ) is recognized to lead to the formation of Criegee intermediates (CIs), which play a key role in controlling the atmospheric budget of hydroxyl radicals and secondary organic aerosols. The reaction network of two CIs with different functionality, i.e. acetaldehyde oxide (CH 3 CHOO) and glyoxal oxide (CHOCHOO) formed in the ozone-assisted oxidation reaction of crotanaldehyde (CA), is investigated over a temperature range between 390 K and 840 K in an atmospheric pressure jet-stirred reactor (JSR) at a residence time of 1.3 s, stoichiometry of 0.5 with a mixture of 1% crotonaldehyde, 10% O 2 , at an fixed ozone concentration of 1000 ppm and 89% Ar dilution. Molecular-beam mass spectrometry in conjunction with single photon tunable synchrotron vacuum-ultraviolet (VUV) radiation is used to identify elusive intermediates by means of experimental photoionization energy scans and ab initio threshold energy calculations for isomer identification. Addition of ozone (1000 ppm) is observed to trigger the oxidation of CA already at 390 K, which is below the temperature where the oxidation reaction of CA was observed in the absence of ozone. The observed CA + O 3 product, C 4 H 6 O 4 , is found to be linked to a ketohydroperoxide (2-hydroperoxy-3-oxobutanal) resulting from the isomerization of the primary ozonide. Products corresponding to the CIs uni- and bi-molecular reactions were observed and identified. A network of CI reactions is identified in the temperature region below 600 K, characterized by CIs bimolecular reactions with species like aldehydes, i.e., formaldehyde, acetaldehyde, and crotonaldehyde and alkenes, i.e., ethene and propene. The region below 600 K is also characterized by the formation of important amounts of typical low-temperature oxidation products, such as hydrogen peroxide (H 2 O 2 ), methyl hydroperoxide (CH 3 OOH), and ethyl hydroperoxide (C 2 H 5 OOH). Detection of additional oxygenated species such as alcohols, ketene, and aldehydes are indicative of multiple active oxidation routes. This study provides important information about the initial step involved in the CIs assisted oligomerization reactions in complex reactive environments where CIs with different functionalities are reacting simultaneously. It provides new mechanistic insights into ozone-assisted oxidation reactions of unsaturated aldehydes, which is critical for the development of improved atmospheric and combustion kinetics models.

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

Tungsten single-atom catalysts for the efficient conversion of isobutene into highly branched liquid hydrocarbons

The catalytic transformation of isobutene into branched liquid hydrocarbons is crucial for the production of reformulated gasoline and fuel additives. Conventional supported catalysts often lack high activity and selectivity toward the desired highly branched dimers and trimers in isobutene oligomerization. Here, by developing a tungsten single-atom catalyst (W SAC ) atomically dispersed on a silica-doped alumina (SDA) support, we report that the W SAC /SDA catalyst enables efficient and selective conversion of isobutene into highly branched C 8 and C 12 liquid olefins while suppressing the formation of heavier hydrocarbons. The atomically dispersed W 1 –O 3 moieties incorporated within the SDA support were synthesized via a high-temperature pyrolysis of a templating zinc metal–organic framework (Zn-MOF) under argon, followed by annealing in static air. The W SAC /SDA catalysts with 1.6–3.7 wt% W loading exhibited single-atom dispersion (∼0.2 nm) and outstanding performance, achieving up to 60% and 95% selectivity to branched C8 olefins at 150 °C and 250 °C, respectively, under ambient pressure. With the demonstrated high activity, selectivity, and stability, the W SAC /SDA catalyst system presents a promising platform for next-generation heterogeneous catalysts for the efficient and selective upgrading of isobutene into high-performance fuel additives.

Branched Olefins↗
DOE OSTI2025

Precursor reaction pathway leading to BiFeO 3 formation: insights from text-mining and chemical reaction network analyses

BiFeO 3 (BFO) is a next-generation non-toxic multiferroic material with applications in sensors, memory devices, and spintronics, where its crystallinity and crystal structure directly influence its functional properties. Designing sol–gel syntheses that result in phase-pure BFO remains a challenge due to the complex interactions between metal complexes in the precursor solution. Here, we combine text-mined data and chemical reaction network (CRN) analysis to obtain novel insight into BFO sol–gel precursor chemistry. We perform text-mining analysis of 340 synthesis recipes with the emphasis on phase-pure BFO and identify trends in the use of precursor materials, including that nitrates are the preferred metal salts, 2-methoxyethanol (2 ME) is the dominant solvent, and adding citric acid as a chelating agent frequently leads to phase-pure BFO. Our CRN analysis reveals that the thermodynamically favored reaction mechanism between bismuth nitrate and 2ME interaction involves partial solvation followed by dimerization, contradicting assumptions in previous literature. We suggest that further oligomerization, facilitated by nitrite ion bridging, is critical for achieving the pure BFO phase.

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

Harnessing ketones as hydrogen acceptors for atom-efficient upgrading of oxygenates to fuels over H/ZSM-5

Heterogeneous mixtures of bio-derived oxygenates are promising feedstocks for synthetic aviation fuel (SAF), but conversion strategies for one common component—short-chain (C 5–7 ) internal ketones—are lacking. Previous work has shown that cyclization of ketones over H/ZSM-5 is limited by its high productivity of light paraffins. We study 4-heptanone upgrading over H/ZSM-5 and show that aromatics and olefins can be formed at high carbon yield when operating at up to 90% conversion. The yield of desirable products is not impacted by the introduction of a recycle stream of the unconverted 4-heptanone and other products with similar boiling points. We hypothesize, based on first-principles calculations, that the higher olefin yield is driven by the ease of hydrogen transfer to unreacted ketones as opposed to hydrogenating olefin products. We demonstrate how this ease of hydrogen transfer to ketones can be leveraged to enhance olefin selectivity in the conversion of methanol to olefins as well by co-feeding ketones. Olefinic products of the cyclization reaction are then oligomerized to a SAF blendstock to demonstrate an end-to-end ketone-to-SAF process facilitated by upgrading ketones over H/ZSM-5 at partial conversion with a recycle stream. The results of this work demonstrate a strategy to improve the carbon yield from bio-derived acids to SAF to over 75%, representing a relative improvement of more than 50% compared to previously reported data.

08 HYDROGEN↗
DOE OSTI2020

Modular repeat protein sculpting using rigid helical junctions

The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.

59 BASIC BIOLOGICAL SCIENCES↗