Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer
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Abstract The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same “compact” fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an “extended” SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.
The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.
Guerbet coupling followed by etherification is a two step process for conversion of ethanol into distillate range molecules. This involves first alcohol oligomerization, followed by acid-catalyzed dehydration. As we will show in this presentation, ethanol can be converted to higher linear and α-branched alcohols by C-C coupling reactions (ethanol oligomerization) as well as to high molecular weight esters by C-O coupling reactions with Cu/MgxAlOy (CuHT) catalysts. Alcohols may be converted to ethers via bimolecular dehydration in a subsequent step. We have identified more than 160 number of species in the products including alcohols, esters, aldehydes, ketonces, and olefins. Alcohols range from C4 to C10. Both alcohols and esters follow a Schulz-Flory chain growth model. We show the relationship between the catalyst properties (BET surface area, acid and base site count and Cu loading and synthesis method) and the performance in the reactions. We also show that physical mixtures of CuHT and HT can have similar product selectivity of low loading CuHT catalysts. The selectivity towards diesel fuel precursor compounds (hereafter ‘DFPC’) increased with conversion until reaching a plateau at high ethanol conversion (~70%). Alcohol selectivity follows a Schultz-Flory distribution at all studied conversions, and that adsorbed ethanol-derived species may undergo surface oligomerization into 1-butanol and higher alcohols before desorbing in a chain-growth mechanism. Zeolite catalysts convert the C4+ alcohols into C8+ ethers in both batch and continuous flow reactors. Selectivities of up to 80% to C8+ ethers at around 70% conversion using a single pass continuous flow system are able to be achieved. The final product feedstocks obtained from etherification have been used in technoeconomic (TEA) and lifecycle analysis (LCA), which indicate a reduction in greenhouse gas (GHG) emissions of 50% relative to conventional diesel. These final feedstocks are undergoing engine testing to elucidate the physiochemical properties and will be compared to diesel #2 ASTM standards as a reference and will serve as a basis to improve the final bio-diesel blendstocks from etherification.
In this presentation we describe the catalytic approaches for conversion of ethanol into diesel fuel ethers. This involves first alcohol oligomerization, followed by acid-catalyzed dehydration. As we will show in this presentation, ethanol can be converted to higher linear and α-branched alcohols by C-C coupling reactions (ethanol oligomerization) as well as to high molecular weight esters by C-O coupling reactions with Cu/MgxAlOy (CuHT) catalysts. Alcohols may be converted to ethers via bimolecular dehydration in a subsequent step. We have identified more than 160 number of species in the products including alcohols, esters, aldehydes, ketones, and olefins. Alcohols range from C4 to C10. Both alcohols and esters follow a Schulz-Flory chain growth model. We show the relationship between the catalyst properties (BET surface area, acid and base site count and Cu loading and synthesis method) and the performance in the reactions. We also show that physical mixtures of CuHT and HT can have similar product selectivity of low loading CuHT catalysts. The selectivity towards diesel fuel precursor compounds (hereafter ‘DFPC’) increased with conversion until reaching a plateau at high ethanol conversion (~70%). Alcohol selectivity follows a Schultz-Flory distribution at all studied conversions, and that adsorbed ethanol-derived species may undergo surface oligomerization into 1-butanol and higher alcohols before desorbing in a chain-growth mechanism. Zeolite catalysts convert the C4+ alcohols into C8+ ethers in both batch and continuous flow reactors. Selectivities of up to 80% to C8+ ethers at around 70% conversion using a single pass continuous flow system are achieved. The final product feedstocks obtained from etherification have been used in technoeconomic (TEA) and lifecycle analysis (LCA), which indicate a reduction in greenhouse gas (GHG) emissions of 50% relative to conventional diesel and diesel fuel prices that are lower than biodiesel. These final feedstocks are undergoing engine testing to elucidate the physiochemical properties and compare well to diesel #2 ASTM standards.
Jet fuel is relatively small in terms of energy consumption and carbon dioxide emissions (10% of U.S. transportation sector in 2021, expected to increase to 14% by 2050). Still airlines have ambitious goals to reduce their greenhouse footprints from carbon-neutral growth beginning this year to reducing greenhouse gas emission for international flights by 50% by 2050 compared to 2005 levels. The challenge is heightened by the longevity of the current fleet (30–50 years) and by the difficulty in electrifying the future fleet because only 5% of the commercial aviation greenhouse gas footprint is from regional flights that might, conceivably be electrified using foreseeable technology. Therefore, large amounts of sustainable aviation fuel will be needed to reach the aggressive targets set by airlines. Only 3 million gallons (11.4 ML) of sustainable aviation fuel (SAF) (with a heat of combustion totaling about 400 TJ = 0.0004 EJ) was produced in the U.S. in 2019 for a 26 billion gallon per year market (3.6 EJ/year). Fischer-Tropsch and ethanol oligomerization (alcohol-to-jet) are considered for producing SAF, including the use of renewable electricity and carbon dioxide. In sequencing the energy transition, cleaning the U.S. grid is an important first step to have the largest greenhouse gas emissions reduction. While carbon dioxide and clean electricity can potentially provide the SAF in the future, an ethanol oligomerization option will require less energy.
Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here, in this work, we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel “dimer of dimers” mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.
Mechanistic investigation of the catalytic conversion of model compounds for plastic pyrolysis oil (1-octene, octadiene, octane, and toluene) over ZSM-5 in a fixed-bed reactor was studied. 1-Octene breaks down into smaller olefins, which undergo further cracking, oligomerization, cyclization, and hydrogen transfer to eventually produce benzene, toluene, xylene (BTX), coke, and hydrogen. The effect of contact time on 1-octene conversion was further investigated and compared with thermodynamics analyses to elucidate the reaction network. Under the reaction conditions (500 oC, 1 atm), octadiene undergoes thermal coking, significantly contributing to reactor fouling. The products from octane cracking are similar to the products from 1-octene conversion whereas toluene undergoes disproportionation, dealkylation and coking. The analysis of spent catalyst showed long-chain hydrocarbons created by oligomerization reactions filled the pores and covered the surface of the catalyst. As a result, when mesoporous ZSM-5 is used instead of conventional, product selectivity is maintained for 70 hours in time-on-stream experiments.
Methane dehydroaromatization (MDA) enables the catalytic conversion of methane into aromatics, mainly benzene, along with hydrogen, in a single-step process under non-oxidative conditions. In this study, we prepared a series of isomorphously substituted Fe-ZSM-5 catalysts with exclusively isolated or low-oligomerized sites up to 3.2% Fe weight loading by adding ethylenediaminetetraacetic acid (EDTA) to the crystallization gel. These catalysts exhibit no induction/activation period and a significantly higher maximum product yield compared to Fe/ZSM-5 catalysts prepared by the incipient wetness impregnation method and containing extensively aggregated FeOx. This investigation focuses on the evolution of Fe sites during the post-synthetic treatments. Most importantly, we demonstrate the quantitative relation between Fe site isolation and catalytic activity, proving that isolated or low-oligomerized Fe species at the exchange sites formed during post-synthetic retreatment are the active sites for methane activation.
Here, this work outlines an optimized process for converting 2,3-butanediol (BDO) into sustainable aviation fuel (SAF) and C4 chemicals. BDO is reactively separated from fermentation broth by forming dioxolanes, which are converted to isobutyraldehyde, methyl ethyl ketone (MEK), and 1,3-butadiene. These intermediates are reduced and dehydrated over Cu/ZSM-5 to form alkenes, which can be oligomerized and hydrotreated to jet-range alkanes. Previous BDO-dioxolane-alkene processes are limited by the requirement for a continuous aldehyde source for dioxolane formation. Brønsted acidic zeolites catalyze dioxolane deacetalization to form isobutyraldehyde and MEK in a >2:1 molar ratio, providing an internal, recyclable aldehyde source. Dioxolane formation optimization was performed to achieve >95% dioxolane yields over Amberlyst-15 and minimize isobutyraldehyde recycle. The overall BDO-dioxolane-fuel process yields an alkane mixture that enables at least a 50% v/v blend with Jet-A. Techno-economic analyses and life cycle assessments for this BDO-dioxolane-fuel process yield scenarios with <$2.50 per gallon gas equivalent and >58% reduction in CO2 emissions.
Flowthrough pretreatment provides valuable insight in the fundamentals of deconstruction of plant biomass. In this study, the potential softwood degradation pathways under water-only and alkali conditions were determined by elucidating the deconstructed biomass-derived products at 0-270 °C for 2-10 min at a flow rate of 25 mL/min with water-only or alkaline at initial pH of 8, 9, 11, and 12, respectively. Results indicated that the initial pH value was a convenient indicator along with the severity parameter to control biomass degradation through the non-oxidative (pH<9) and oxidative (pH=9) pathways. Up to 100 % of hemi-sugars, 90 % of cellulose, and 70 % of lignin were derived from softwood under non-oxidative conditions at severity parameter LogR0 around 5.5, respectively. On the contrary, at pH 12, the oxidative degradation resulted in pretreated hydrolysate rich in monomeric and oligomeric phenolic products as well as glycolic acid, acetic acid, and formic acid from carbohydrates. The two dimensional 1H-13C heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) analysis revealed that non-oxidative degradation at initial pH values lower than 9 mainly cleaved ß-O-4, all of the ß-ß, and ß-5/a-O-4 linkages, whereas substantial aromatic ring structures with limited ß-O-4 structures remaining at pH 12 through oxidative degradation.
External stressors modulate the oligomerization state of photosystem I (PSI) in cyanobacteria. The number of red chlorophylls (Chls), pigments lower in energy than the P700 reaction center, depends on the oligomerization state of PSI. Here, we use ultrafast transient absorption spectroscopy to interrogate the effective connectivity of the red Chls in excitonic energy pathways in trimeric PSI in native thylakoid membranes of the model cyanobacterium Synechocystis sp. PCC 6803, including emergent dynamics, as red Chls increase in number and proximity. Fluence-dependent dynamics indicate singlet–singlet annihilation within energetically connected red Chl sites in the PSI antenna but not within bulk Chl sites on the picosecond time scale. These data support picosecond energy transfer between energetically connected red Chl sites as the physical basis of singlet–singlet annihilation. The time scale of this energy transfer is faster than predicted by Förster resonance energy transfer calculations, raising questions about the physical mechanism of the process. Our results indicate distinct strategies to steer excitations through the PSI antenna; the red Chls present a shallow reservoir that direct excitations away from P 700 , extending the time to trapping by the reaction center.
Supported vanadium oxide catalysts are important industrial materials for a wide array of chemical transformations. The condition of surface hydration is of particular interest as a reflection of the state of a freshly manufactured catalysts prior to its activation in catalytic reactors or under conditions of photocatalysis where surface vandia are exposed to moisture. Under such conditions, the surface vanadia species undergo structural changes as evidenced by 51 V MAS NMR in this study. For low surface vanadia densities on titania, a modest trend towards the formation of dimeric and oligomeric vanadia species was observed under hydrated conditions when compared to the corresponding dehydrated catalyst, which contains a large abundance of monomeric vanadia species. The incorporation of tungsten oxide to the V 2 O 5 /TiO 2 catalyst with low surface vanadia density, however, is found to better stabilize the surface vanadia species on the titania support upon hydration than its tungsta-free counterpart. This stabilization is not an intrinsic property of more extensively oligomerized surface vanadia species in the presence of tungsten oxide, evidenced by conditions of high concentrations of surface vanadia oligomers on titania that exhibit dramatic structural changes upon hydration. At high surface vanadia coverage under hydrated environments, the simultaneous observation of crystalline V 2 O 5 nanoparticles and a mobile phase of surface vanadia species is apparent, where vanadia species are dissolved in the thin hydration layer on the titania support. These new findings have broad implications on the behavior of other metal oxide species on high surface oxide supports under hydrated conditions.
Molecular and oligomeric amines supported in porous oxide supports are a promising class of CO 2 sorbent materials studied for CO 2 removal from diverse streams such as flue gas and ambient air. Among the various amines investigated, low molecular weight, hyperbranched poly(ethyleneimine) (PEI), and tetraethylenepentamine (TEPA) are among the most extensively studied. While macroscopic structure–performance relationships relating the support structure, amine loading, and other factors affecting CO 2 sorption capacities and kinetics have been developed, structural and dynamic information about the organic amine phase in the porous support is less plentiful. The structure and mobility of amines impregnated in the pores of porous supports directly impact gas sorption, as the accessibility of amine sites in the pores directly relates to amine distribution in the pores and overall pore filling as well as the dynamics of the amine chains. Here, we prepare a family of mesoporous silica SBA-15 materials containing varying loadings of oligomeric (PEI) and molecular (TEPA) amines. 1 H T 1 –T 2 relaxation correlation solid-state NMR experiments are used to characterize the structural and dynamic properties of the confined amines. Both TEPA and PEI are shown to form multiple different domains in the pores, each with distinguishable dynamic properties. TEPA and PEI form more rigid layers around the silica support walls at lower organic loading fractions, characterized by lower mobilities, followed by the formation of more mobile domains less engaged in pore wall interactions at higher loadings. TEPA shows faster mobilities than PEI because of its lower molecular weight. TEPA also appears to more easily transfer between domains within the pores, leading to generally faster CO 2 uptake rates with higher sorption capacities, while PEI located closer to the pore walls remained much less mobile and is thus less engaged in CO 2 capture.
Here, we study the phase behavior of a triblock organic–inorganic hybrid copolymer, poly(polyhedral oligomeric silsesquioxane)-b-poly(ethylene oxide)-b-poly(polyhedral oligomeric silsesquioxane) (POSS-PEO-POSS)/lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt mixture, as a function of temperature. The polymer exhibits a lamellar morphology both in the neat state and in the presence of salt. However, the average grain size increases substantially when the electrolyte is heated above 113 °C. The grain structure of this sample changes reversibly with temperature, that is, smaller grains reappear when the electrolyte is cooled below 113 °C. While annealing block copolymers at high temperatures often leads to an increase in the grain size, this change is generally irreversible. The reason for the reversible change in the grain structure of the POSS-PEO-POSS/LiTFSI electrolyte is discussed. The ionic conductivity of the electrolyte also exhibits reversible changes in this temperature window. Knowledge of the grain structure is crucial for understanding ion transport in nanostructured electrolytes.
Supported V2O5-WO3/TiO2 materials employed as selective catalytic reduction (SCR) catalysts for NOx emission control from power plants. Fresh SCR catalysts usually receive exposure to harsh treatments in industry to accelerate catalyst activation (calcination in air at 650oC) and catalyst aging (hydrothermal aging at 650oC) in a way that represents various points in the catalyst/product lifetime. The present study investigates the catalyst structural and chemical changes occurring during such harsh treatments. Three series of supported V2O5-WO3/TiO2 catalysts were prepared by incipient-wetness impregnation of aqueous ammonium metavanadate and metatungstate precursors. The catalysts were subsequently dried and calcined at 550oC in O2, 650oC in O2, and hydrothermal conditions (10% O2, 8% H2O, 7% CO2 and 75% N2) at 650oC. The resulting catalysts were physically characterized by numerous techniques (in situ Raman, in situ IR, in situ High Field-High Spinning solid-state 51V MAS NMR, in situ EPR, XRD, BET surface area and ICP) and chemically probed with adsorbed ammonia, SCR-TPSR, and the SCR reaction. The surface WOx sites on the TiO2 support behave as a textural promoter that stabilizes the TiO2 (anatase) phase from sintering and transforming to the undesirable crystalline TiO2 (rutile) phase that can lead to formation of a Ti1-xVxO2 (rutile) solid solution with reduced V4+ cations (~7-15%). The surface VOx sites are mostly oligomerized as surface V+5Ox sites (~50-85% oligomers) and the extent of oligomerization tends to increase with surface WOx coverage and calcination temperature. A major difference between the calcined and hydrothermally treated catalysts was the low concentration of surface NH3* species on Lewis acid sites for the hydrothermally treated catalysts, yet the SCR activity was almost comparable for both catalysts. This finding suggests that surface NH4+*, primarily associated with the surface VOx sites, are able to efficiently perform the SCR reaction. Given that multiple catalyst parameters were simultaneously varying during these treatments, it was difficult to correlate the SCR activity with any single catalyst parameter. A correlation, however, was found between the SCR TOF/activity and the sum of the surface NH3* and NH4+* species, which is dominated by the surface NH4+* species.
Criegee intermediates (CIs) are central to the ozonolysis of unsaturated organic compounds, controlling the formation of small fragmentation reaction products and higher molecular weight oligomeric compounds through competing unimolecular and bimolecular pathways. In particular, the reaction of thermalized CI with carboxylic acids (RCOOH) to produce oligomeric α-acyloxyalkyl hydroperoxides (AAHPs) is of interest to the chemical transformation of organic compounds in the atmosphere. In the gas phase, the CI + RCOOH reaction proceeds at supercollisional rates, consistent with a barrierless reaction mechanism. However, the rate of this reaction in condensed phases remains uncertain. Here, we report the results of aerosol flow tube studies of the ozonolysis of submicron organic aerosol containing mixtures of an internal n-alkene (Z-9-tricosene, tri) and a saturated acid (2-hexyldecanoic acid, HDA). The decay of the reactants and formation of reaction products are monitored using atmospheric pressure chemical ionization mass spectrometry (APCI–MS). A 6-fold decrease in the reactive uptake of ozone is observed with increasing acid concentration, consistent with a previous study using alcohol additives. The decay of HDA with ozone exposure shows that HDA scavenges CIs at rates comparable to competing unimolecular pathways involving CIs. The decay kinetics of HDA are analyzed using a simple kinetic model in order to constrain the ratio of the CI + RCOOH and unimolecular CI rate constants. Empirical fitting to this model, combined with theoretical estimates of the unimolecular loss rate, yields a CI + RCOOH rate constant of 1.85 ± 0.27 × 10 –19 cm 3 molec –1 s –1 , which is six orders of magnitude slower than the expected diffusion limit in a liquid organic matrix. Stochastic kinetic simulations are conducted with different values of the CI + RCOOH rate constant to validate this result and show that the diffusion-limited rate is indeed much too rapid to reproduce the experimental results.
Here, we developed a tandem, unassisted, solar-driven electrochemical and photothermocatalytic process for the single-pass conversion of CO 2 to butene using only simulated solar irradiation as the energetic input. The two-step process involves electrochemical CO 2 reduction (CO 2 R) to ethylene followed by ethylene dimerization to butene. We assessed two unassisted electrochemical setups to concentrate ethylene in the CO 2 R reactor, achieving concentrations up to 5.4 vol.% with 1.8% average solar-to-ethylene conversion and 5.6% average CO 2 -to-ethylene single-pass conversion under 1-sun illumination. When passed through the photothermocatalytic ethylene oligomerization reactor, we generated 600 ppm of butene under 3-sun illumination. Through analysis of this process, we identified that the presence of H 2 , CO, and H 2 O leads to rapid deactivation of the Ni-based ethylene oligomerization catalyst.