Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a ‘pedal bin’ mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis

Highly Selective Condensation of Biomass-Derived Methyl Ketones as a Source of Aviation Fuel

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. The Back Cover shows a depiction of the carbon cycle for a tunable set of chemistry that can be used to synthesize exceptional jet fuel via n-alkyl methyl ketones. In this work, methyl ketones, which can be derived from biomass in either chemical or hybrid biological-chemical pathways, are selectively transformed to cyclic trimers by aldol condensation and Michael addition. By altering the ratio of starting methyl ketones, an alkane blend can be generated after hydrodeoxygenation that not only satisfies the low freezing point necessary for jet fuel, but also the broad volatility distribution typical of petroleum-derived fuels. The carbon generated by combustion of these fuels then produces further biomass, completing the carbon cycle. More details can be found in the Full Paper by Sacia etal. (DOI: 10.1002/cssc.201500002)

Hybrid Biological-Chemical Approach Offers Flexibility and Reduces the Carbon Footprint of Biobased Plastics, Rubbers, and Fuels

A critical challenge for the bioenergy research community has been producing drop-in hydrocarbon fuels and chemicals at yields sufficient to compete with their petroleum-derived counterparts. Biological production of highly reduced compounds poses fundamental challenges. Conversely, glucose, xylose, and sucrose can be fermented to ethanol at near-theoretical yields. Just as olefin crackers are often considered a gateway for petrochemical complexes that produce an array of downstream products, catalytic ethanol upgrading can potentially enable an entire biorefining complex able to produce renewable, low-carbon fuels and chemicals. By doping the Ta2O5/SiO2 catalyst with different transition metals, we show that Ostromyslensky catalysts can be utilized for direct conversion of ethanol to varying ratios of 1,3-butadiene (1,3-BD), dietheylether (DEE), and ethylene. These results are integrated into the first comprehensive analysis of ethanol conversion to 1,3-BD, DEE, and ethylene that incorporates empirical data with chemical process modeling and life-cycle greenhouse gas (GHG) assessment. We find that the suite of products can replace conventional rubber, plastics, and diesel, achieving as much as a 150% reduction in GHG-intensity relative to fossil pathways (net carbon sequestration). Selecting the route with the greatest ethylene and DEE output can maximize total potential emission reductions

Hybrid Biological-Chemical Approach Offers Flexibility and Reduces the Carbon Footprint of Biobased Plastics, Rubbers, and Fuels

A critical challenge for the bioenergy research community has been producing drop-in hydrocarbon fuels and chemicals at yields sufficient to compete with their petroleum-derived counterparts. Biological production of highly reduced compounds poses fundamental challenges. Conversely, glucose, xylose, and sucrose can be fermented to ethanol at near-theoretical yields. Just as olefin crackers are often considered a gateway for petrochemical complexes that produce an array of downstream products, catalytic ethanol upgrading can potentially enable an entire biorefining complex able to produce renewable, low-carbon fuels and chemicals. By doping the Ta2O5/SiO2 catalyst with different transition metals, we show that Ostromyslensky catalysts can be utilized for direct conversion of ethanol to varying ratios of 1,3-butadiene (1,3-BD), dietheylether (DEE), and ethylene. These results are integrated into the first comprehensive analysis of ethanol conversion to 1,3-BD, DEE, and ethylene that incorporates empirical data with chemical process modeling and life-cycle greenhouse gas (GHG) assessment. We find that the suite of products can replace conventional rubber, plastics, and diesel, achieving as much as a 150% reduction in GHG-intensity relative to fossil pathways (net carbon sequestration). Selecting the route with the greatest ethylene and DEE output can maximize total potential emission reductions

Selectivity tuning over monometallic and bimetallic dehydrogenation catalysts: Effects of support and particle size

The efficacy of tandem dehydrogenation-condensation catalysts for the upgrade of bio-derived intermediates is largely determined by their relative (de-)hydrogenation and decarbonylation activity. Here, the effects of support and particle size of heterogeneous PdCu alloy catalysts on (de-)hydrogenation and decarbonlylation reactions were investigated using kinetic measurements, X-ray absorption spectroscopy and density functional theory (DFT). The chemical mismatch of Cu2+ with Ti4+ and Ca2+ prevents the substitution of Cu into the lattice of TiO2 or hydroxyapatite supports, and facilitates its alloying with Pd, resulting in improved selectivity for hydrogenation-dehydrogenation reactions compared to decarbonylation reactions. Based on kinetic measurements of butyraldehyde reactions over Pd and PdCu/SiO2 model catalysts, decarbonylation activity is attributed to the presence of Pd surface ensembles, while (de-)hydrogenation reactions are catalyzed by PdCu sites on the surface. This is consistent with selectivity and CO coverage trends with increasing conversion, and DFT-based microkinetic modeling. Selectivity control can also be achieved using the PdCu nanocluster size. Smaller nanoparticles favor the C-CO bond scission step of the decarbonylation reaction, due to the stronger binding of CO and alkyl species to sites of lower coordination. CO-induced segregation of reactive Pd atoms to under-coordinated step/edge sites also amplifies the geometric effect on the catalytic behavior

Selectivity tuning over monometallic and bimetallic dehydrogenation catalysts: Effects of support and particle size

The efficacy of tandem dehydrogenation-condensation catalysts for the upgrade of bio-derived intermediates is largely determined by their relative (de-)hydrogenation and decarbonylation activity. Here, the effects of support and particle size of heterogeneous PdCu alloy catalysts on (de-)hydrogenation and decarbonlylation reactions were investigated using kinetic measurements, X-ray absorption spectroscopy and density functional theory (DFT). The chemical mismatch of Cu2+ with Ti4+ and Ca2+ prevents the substitution of Cu into the lattice of TiO2 or hydroxyapatite supports, and facilitates its alloying with Pd, resulting in improved selectivity for hydrogenation-dehydrogenation reactions compared to decarbonylation reactions. Based on kinetic measurements of butyraldehyde reactions over Pd and PdCu/SiO2 model catalysts, decarbonylation activity is attributed to the presence of Pd surface ensembles, while (de-)hydrogenation reactions are catalyzed by PdCu sites on the surface. This is consistent with selectivity and CO coverage trends with increasing conversion, and DFT-based microkinetic modeling. Selectivity control can also be achieved using the PdCu nanocluster size. Smaller nanoparticles favor the C-CO bond scission step of the decarbonylation reaction, due to the stronger binding of CO and alkyl species to sites of lower coordination. CO-induced segregation of reactive Pd atoms to under-coordinated step/edge sites also amplifies the geometric effect on the catalytic behavior

ABE Condensation over Monometallic Catalysts: Catalyst Characterization and Kinetics

Herein, we present work on the catalyst development and the kinetics of acetone-butanol-ethanol (ABE) condensation. After examining multiple combinations of metal and basic catalysts reported in the literature, Cu supported on calcined hydrotalcites (HT) was found to be the optimal catalyst for the ABE condensation. This catalyst gave a six-fold increase in reaction rates over previously reported catalysts. Kinetic analysis of the reaction over CuHT and HT revealed that the rate-determining step is the C−H bond activation of alkoxides that are formed from alcohols on the Cu surface. This step is followed by the addition of the resulting aldehydes to an acetone enolate formed by deprotonation of the acetone over basic sites on the HT surface. The presence of alcohols reduces aldol condensation rates, as a result of the coverage of catalytic sites by alkoxides

ABE Condensation over Monometallic Catalysts: Catalyst Characterization and Kinetics

Herein, we present work on the catalyst development and the kinetics of acetone-butanol-ethanol (ABE) condensation. After examining multiple combinations of metal and basic catalysts reported in the literature, Cu supported on calcined hydrotalcites (HT) was found to be the optimal catalyst for the ABE condensation. This catalyst gave a six-fold increase in reaction rates over previously reported catalysts. Kinetic analysis of the reaction over CuHT and HT revealed that the rate-determining step is the C−H bond activation of alkoxides that are formed from alcohols on the Cu surface. This step is followed by the addition of the resulting aldehydes to an acetone enolate formed by deprotonation of the acetone over basic sites on the HT surface. The presence of alcohols reduces aldol condensation rates, as a result of the coverage of catalytic sites by alkoxides