Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6
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Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Here, our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.
This dataset supports a publication, "Surface Protected Organozirconium Catalyzes C–H Alumination of Saturated Hydrocarbons", and describes the surface-organozirconium catalyzed exchange of ethyl group in AlEt3 for dodecyl or methyl from dodecane or methane. The research describes the benefits of capping remaining surface OH with SiMe3 for improving yields and turnovers. The dataset includes characterization of the precatalyst using solid-state nuclear magnetic resonance spectroscopy and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), as well as gas chromatography and solution NMR of reaction products.
Programmable catalysts exhibiting forced oscillation in the free energy of reacting surface species were simulated to understand the general mechanisms leading to efficient use of the input energy. Catalytic ratchets with either positive or negative adsorbate scaling exhibited oscillation conditions of both high and low turnover efficiency, yielding catalytic turnover frequencies either close to or significantly lower than the applied catalyst oscillation frequency, respectively. The “effective rate”, defined as the product of the catalytic turnover frequency and the turnover efficiency (ηTOE), was limited via two catalytic mechanisms: a leaky catalytic ratchet existed when molecules repeatedly traversed backward through the catalytic transition state upon catalyst oscillation, while a catalytic ratchet with low surface participation exhibited reduced formation of a gas-phase final product due to low surface product coverage. Furthermore, a single applied frequency yielding a maximum effective catalytic rate defined as the “resonance frequency” provided maximum combined benefit for catalytic rate and efficiency.
Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.
Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.
In this study, the catalytic pyrolysis of low-density polyethylene (LDPE), polyethylene terephthalate (PET) and their mixture (1 : 1 wt/wt) with three zeolite catalysts (HZSM-5, H-beta, HY) was investigated using a thermogravimetric analyzer (TGA) and a Pyroprobe® micro-reactor coupled to a gas chromatograph mass spectrometer (Py-GC/MS). The TGA results demonstrated that during pyrolysis at 10 °C min –1 , on average, zeolite catalysts decreased the maximum decomposition temperature by 149 °C for LDPE while only decreasing by 8 °C for PET. The derivative thermogravimetric (DTG) curve evidenced interactions when the two polymers were catalytically co-pyrolyzed for all the three catalysts. A lumped nth order reaction scheme was able to accurately model both non-catalytic and catalytic pyrolysis and co-pyrolysis by using the least squares fitting approach for determining the kinetic parameters. The kinetic model was able to model well the interaction effects observed during catalytic co-pyrolysis of LDPE and PET with HZSM-5, H-beta, and HY (Fit% Wt% > 96%, Fit% DTG > 94%). Py-GC/MS experiments for the catalytic fast pyrolysis of LDPE revealed that HZSM-5 resulted in the highest selectivity to aromatic hydrocarbons (31.6%) and HY resulted in the highest selectivity to gasoline range C 5 –C 10 paraffins and olefins (40.9%). Catalytic fast pyrolysis of PET showed high selectivity to benzene for all the catalysts (>43%) and that HZSM-5 resulted in the highest selectivity to polyaromatic hydrocarbons (24.7%). Finally, the catalytic fast co-pyrolysis of LDPE and PET revealed interaction effects for all the three catalysts evidenced by a positive synergy% for alkylated benzenes (3–142%) and polyaromatics (105–187%) with a concomitant negative synergy% for benzene (24–36%) and C 5 –C 10 paraffins and olefins (27–53%).
Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.
Catalytic condensers stabilize charge on either side of a high-k dielectric film to modulate the electronic states of a catalytic layer for the electronic control of surface reactions. Here, carbon sputtering provided for fast, large-scale fabrication of metal–carbon catalytic condensers required for industrial application. Carbon films were sputtered on HfO 2 dielectric/p-type Si with different thicknesses (1, 3, 6, and 10 nm), and the enhancement of conductance and capacitance of carbon films was observed upon increasing the carbon thickness following thermal treatment at 400 °C. After Pt deposition on the carbon films, the Pt catalytic condenser exhibited a high capacitance of ∼210 nF/cm 2 that was maintained at a frequency ∼1000 Hz, satisfying the requirement for a dynamic catalyst to implement catalytic resonance. Temperature-programmed desorption of carbon monoxide yielded CO desorption peaks that shifted in temperature with the varying potential applied to the condenser (−6 or +6 V), indicating a shift in the binding energy of carbon monoxide on the Pt condenser surface. A substantial increase in capacitance (∼2000 nF/cm 2 ) of the Pt-on-carbon devices was observed at elevated temperatures of 400 °C that can modulate ∼10% of charge per metal atom when 10 V potential was applied. A large catalytic condenser of 42 cm 2 area Pt/C/HfO 2 /Si exhibited a high capacitance of 9393 nF with a low leakage current/capacitive current ratio (<0.1), demonstrating the practicality and versatility of the facile, large-scale fabrication method for metal–carbon catalytic condensers.
Catalytic bias refers to the relative rate preference of a catalyst for either the forward or reverse direction. In enzymatic metal cofactor-based oxidation-reduction catalysis, the tuning of catalytic bias plays an underlying role in controlling rates of reactivity. For this, enzymes have evolved complex active sites that can exist in multiple oxidation states with differing reduction potentials in order to achieve challenging multi-step, oxidation-reduction reactions. Conceivably, the relative stability of the intermediates that contribute to determining the rate-limiting step of the catalytic cycle could impose catalytic bias, although mechanisms for this concept are just beginning to be realized. As one example, recent work on Clostridium pasteurianum [FeFe]-hydrogenases which catalyze reversible hydrogen oxidation have shown that the differential stabilization/destabilization of active site oxidation states through either static or dynamic protein interactions can preferentially promote either the hydrogen oxidation or proton reduction direction of the reaction. This revealed how an enzymatic cofactor can impose bias in oxidation-reduction catalysis through various tuning mechanisms by protein scaffold interactions. The hypothesis based on achieving catalytic bias through the modulation of cofactor oxidation states critical for the reaction cycle can be extended more generally to other cofactor-based oxidation-reductions catalysts. The current understanding of catalytic bias has significant implications for the design of synthetic catalysts used in industrial settings, as well as providing a greater fundamental understanding of the factors that control metabolic processes in all life.
Catalytic conversion of waste rubbers and plastics into aromatic hydrocarbons is a promising approach to waste management and energy recovery. In the present study, acidic HY zeolites were supported by cobalt, iron, and zirconium, and the catalysts were characterized by powder X-ray diffraction, nitrogen adsorption-desorption, ammonia temperature programmed desorption, X-ray photoelectron spectroscopy, and pyridine-Fourier transform infrared spectroscopy. Here, the catalytic degradation of waste polybutadiene rubbers (BR) was conducted to investigate the degradation mechanism and evaluate the catalytic activity of supported zeolites. Experimental results indicated that HY loaded by zirconium and iron led to a higher content of Lewis acid sites as opposed to cobalt supported one. Compared with the non-catalytic pyrolysis of BR, the zirconium supported HY (Zr/HY) led to a 10-fold increase in aromatic hydrocarbons production with a distinctively high selectivity of 97.9%. A series of waste polymers including waste tires (WT), polyethylene (PE), polycarbonate (PC), and BR, were subjected to catalytic pyrolysis to explore the effects of polymer type on aromatic hydrocarbons generation, and BR was the most effective substrate, with yield enhancement reaching 2.4 over Zr/HY. Catalytic co-pyrolysis of waste rubbers and plastics was conducted to probe the effect of polymer structure on aromatic hydrocarbons formation, where a significant synergistic effect was observed in the PE co-fed with PC run.
RTI has developed a catalytic fast pyrolysis (CFP) process to produce biomass-based hydrocarbon replacement fuels. From a technology perspective, this advanced biofuels process produces liquid transportation fuels that can leverage capital expenditures in the existing petroleum distribution infrastructure. From a business perspective, this technology does not face potential market limitations caused by oxygenate blend limitations for light duty vehicle applications. A promising catalyst has been developed with excellent potential for deoxygenation to produce a hydrocarbon-rich biocrude that is more suitable for upgrading with traditional hydroprocessing technology. The role of the catalyst is to control the chemistry during biomass pyrolysis to produce a biocrude in a single step that has lower oxygen content and is more thermally stable than conventional biomass fast pyrolysis oil. Catalyst properties are optimized to minimize gas and coke production and improve catalytic deoxygenation and biocrude yields. Results from this project have demonstrated that biocrudes from catalytic fast pyrolysis contain <20 wt% oxygen, with the organic fraction as low as 12% oxygen. These oxygen numbers are > 50% lower compared to traditional fast pyrolysis oils. The biocrude produced from our CFP process can be upgraded to gasoline range hydrocarbons. A very conservative approach for upgrading included a preliminary stabilization step followed by a hydroprocessing step. The oxygen content in the upgraded product was decreased by 97% (to less than 3wt %) from the oxygen content of the biocrude sample. Additionally, the acid content was reduced by 99% from the acid content of the biocrude sample. In an optimized integrated process, the CFP step and the hydroprocessing (upgrading) step need to be carefully balanced to maximize the input biomass energy that is recovered in the finished biofuels. Hydrogen utilization and carbon recovery during both catalytic biomass pyrolysis and biocrude upgrading need to be optimized to maximize energy recovery in the finished biofuel. A nominal 1 ton per day (TPD) catalytic biomass pyrolysis system was designed based on the laboratory experimental data. The system was designed to achieve the short residence times (0.5–2 sec) and high heat transfer rates required for maximum liquid biocrude yields while optimizing process integration to maintain catalyst activity by continuous regeneration. The catalytic biomass pyrolysis reactor is a continuously circulating single-loop transport reactor design that is flexible enough to allow sensitivity studies around temperature, residence time, biomass feed rate, and catalyst-to-biomass ratio (i.e., catalyst circulation rate) for process optimization. For a nominal 100 lb/hr feed rate of dry biomass, the products include ~25 lb/hr char and coke, ~20 lb/hr permanent gases, and ~55 lb/hr condensable vapors. Pyrolysis temperatures are 350–600°C, and the system is operated close to ambient pressure. Production of the catalyst developed within the project was scaled up to provide enough material (200kg) for bench-scale testing. The 1TPD bench-scale unit was fabricated, installed and commissioned with this project. Biocrude samples from wood were produced in this unit with the CFP catalyst with material balance > 90%. The intermediate biocrude yields and chemical composition compare well with previous laboratory results and a hydroprocessing strategy for upgrading the resulting biocrude was developed. The experimental results obtained within this project were used to develop a process model for a 2000 TPD commercial facility. Detailed flow sheets were developed for all major unit operations in the process and provided a basis for an economic analysis to develop capital and operating costs. Estimates of the biofuel production costs were used to develop internal rates of return for the yields and compositions measured for the current state of technology at the end of this project and for the yields anticipated for an optimized (nth plant) scenario as additional process improvements are made.
Microwave-assisted catalytic conversion of waste feedstocks to fuels and value-added chemicals shows incredible promise as an efficient pathway to support the U.S. Department of Energy’s vision toward strengthening the nation’s energy independence. Microwave-heated systems have the potential to outperform conventional technologies through energy-efficient heating and improved product selectivity. This chapter emphasizes microwave-assisted catalytic approaches for waste conversion, allowing maximum energy recovery and extraction of valuable chemicals from waste feedstock such as biomass and plastics while reducing undesired byproducts. A gap remains in understanding how microwaves interact with materials to enable rapid and selective heating, which is crucial for improving catalytic efficiency. This chapter attempts to address this knowledge gap by proposing mechanisms that explain the microwave-catalytic interactions for efficient conversion of biomass-plastic wastes. In addition, comparisons with conventional catalytic technologies as well as the potential for scale ups and future commercialization of microwave-catalytic waste conversion technologies are also discussed.
Thermochemical conversion of plastic wastes is a promising approach to produce alternative energy-based fuels. Herein, we conducted catalytic fast co-pyrolysis of polycarbonate (PC) and polystyrene (PS) to generate aromatic hydrocarbons using HZSM-5 (Zeolite Socony Mobil-5, hydrogen, Aluminosilicate) as a catalyst. The results indicated that employing HZSM-5 in the catalytic conversion of PC facilitated the synthesis of aromatic hydrocarbons in comparison to the non-catalytic run. A competitive reaction between aromatic hydrocarbons and aromatic oxygenates was observed within the studied temperature region, and catalytic degradation temperature of 700 °C maximized the competing reaction towards the formation of targeted aromatic hydrocarbons at the expense of phenolic products. Catalyst type also played a vital role in the catalytic decomposition of PC wastes, and HZSM-5 with different Si/Al molar ratios produced more aromatic hydrocarbons than HY (Zeolite Y, hydrogen, Faujasite). Regarding the effect of Si/Al molar ration in HZSM-5 on the distribution of monocyclic aromatic hydrocarbons (MAHs), a Si/Al molar ratio of 38 maximized benzene formation with an advanced factor of 5.1. Catalytic fast co-pyrolysis of PC with hydrogen-rich plastic wastes including polypropylene (PP), polyethylene (PE), and polystyrene (PS) favored the production of MAHs, and PS was the most effective hydrogen donor with a ~2.5-fold increase. The additive effect of MAHs increased at first and then decreased when the PC percentage was elevated from 30 % to 90 %, achieving the maximum value of 32.4 % at 70 % PC.
The integration of catalysts onto the surface of membranes enables simultaneous physical separation and catalytic transformation of constituents in a feed stream, facilitating improved contaminant removal and fouling mitigation. Distillation membranes are a particularly attractive platform for catalytic membranes because they reject nonvolatile species and exhibit exceptional resistance to oxidative and radical-driven degradation. However, imparting catalytic functionality onto hydrophobic, porous distillation membranes has proven challenging since the membranes used are chemically inert and difficult to modify. Furthermore, catalysts on the membrane surface can decrease hydrophobicity and increase the membrane’s susceptibility to pore wetting and failure. In this work, we create a catalytic distillation membrane by coating a polytetrafluoroethylene membrane surface with titanium dioxide (TiO 2 ) via plasma-assisted atomic layer deposition (ALD). By precisely tuning the ALD parameters, we demonstrate localized growth of TiO 2 near (within approximately 1 μm) the surface of polytetrafluoroethylene membranes, forming a catalytically active interface while preserving the underlying hydrophobic pore structure. Localized growth of TiO 2 is confirmed by electron microscopy and spectroscopy techniques, and membranes coated with 500 cycles of ALD show pressure tolerance up to 12.8 bar and higher than 95% salt rejection in pressure-driven distillation. Photocatalytic activity is demonstrated via the degradation of methylene blue dye under UV irradiation, where increasing TiO2 loading leads to an enhancement in dye degradation. These results establish a general strategy for integrating catalytic functionality into chemically inert, hydrophobic membranes without compromising distillation performance, providing a pathway toward multifunctional membranes that couple advanced oxidation with membrane separation for water treatment.
Platinum-based supported catalysts for hydrocarbon conversion are among the most effective for selective dehydrogenation and isomerization processes. However, high process temperatures and the possibility of coke formation require catalyst modifications to mitigate such effects. One of the emerging approaches to prevent platinum catalyst deactivation is the use of boron additives that have been proposed to prevent coking. Despite such a valuable property of boron, the mechanisms for extending the catalyst lifetime and the decrease in coke formation based on this method are still poorly understood. The type and transformations of boron species on silica surface were investigated as a function of boron introduction, platinum addition, catalyst activation, and catalytic reactivity by a combination of X-ray photoelectron spectroscopy, electron microscopy, solid-state nuclear magnetic resonance spectroscopy, and density functional theory calculations to uncover the possible role of boron modification in improving the catalytic performance. Catalytic nonoxidative dehydrogenation of n-butane revealed that incorporation of boron improved the catalytic activity (similar to 3x) and stability of Pt/SiO 2 . The role of boron in enhancing catalytic performance was attributed to facilitating the migration of alkyl groups from platinum catalytic centers to tetrahedrally coordinated boron sites.
Rational catalyst design remains a significant challenge, with electronic structure, steric, and electrostatic effects known to contribute to activity. Recently, dynamics has been recognized as another factor that impacts catalysis, though identifying and predicting these effects has remained out of reach. Nickel-substituted rubredoxin (NiRd), a protein-based mimic of a hydrogenase enzyme, serves as a model catalytic system in which dynamics can be systematically investigated with respect to activity. While over 30 secondary-sphere mutants of NiRd have been shown to be catalytically active, no significant correlation was observed between the rates and catalytic overpotential or electronic structure, prompting questions about the protein-derived factors that modulate activity. Here, in this work, NMR spectroscopy was used to investigate the roles of substrate accessibility, protein dynamics, and protein stability in controlling catalysis. Significant paramagnetic effects from the nickel center (S = 1) isolate the methylene proton resonances of the metal-coordinating cysteine residues. The sensitivity of resonance positions and linewidths to local environment offers an opportunity to study dynamical molecular changes around the metal center with high resolution. Machine learning algorithms were employed to identify correlations between the catalytic activity and the paramagnetic NMR spectra. These analyses revealed spectroscopic features of specific cysteine protons that report on catalytic overpotential and increased turnover rates, which are further supported by the results obtained using high-field NMR techniques. Collectively, these studies indicate the potential for multifrequency NMR techniques to resolve key contributors to catalytic activity and highlight the importance of local and outer-sphere dynamics.
Single-atoms (SAs) with atomically coordinated reaction centers are considered the next generation of catalysts that can exhibit exceptional catalytic efficiency. However, the general concern about thermodynamic vulnerabilities of SAs questions their practical value. Moreover, whether the inherent catalytic nature of SAs is superior compared with that of larger nanoparticles is still under debate. Here, we address two controversies by a comparative study using two catalysts: Pt/TiO 2 and Pt/CeO x –TiO 2 . Based on a hierarchical study of density functional theory, time-resolved catalysis performance test, in situ infrared spectroscopy, and operando X-ray absorption spectroscopy, we could unveil the catalytic nature of Pt-SAs and their stability. By utilizing the heterogeneous interface formed between TiO 2 supporting particles and CeO x clusters formed on the surface of TiO 2 , we preferentially synthesized Pt-SAs pinned at the CeO x –TiO 2 interfaces on CeO x –TiO 2 hybrid-oxide supports. The strong electronic coupling between the Pt-SAs and the Ce ions at the CeO x –TiO 2 interfaces enhanced the catalytic activity toward CO oxidation of Pt-SAs and improved the long-term stability under CO oxidation conditions. The CO oxidation activity of Pt-SAs stabilized at CeO x –TiO 2 was improved by 13.5 times at 200 °C compared with the Pt-SAs on TiO 2 . The results present how to easily improve the activity and stability of Pt-SAs using a simple interface control method. Moreover, we demonstrate that the catalytic activity and the stability of Pt-SAs can be monitored through the chemical state of the interfaces. Finally, our study provides comprehensive understanding about the catalytic nature as well as a novel strategy toward applications of Pt-SAs, enabling sustainable use of Pt in heterogeneous catalysts.