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At least 37 records · Page 2

High efficiency tantalum-based ceramic composite structures

Tantalum-based ceramics are suitable for use in thermal protection systems. These composite structures have high efficiency surfaces (low catalytic efficiency and high emittance), thereby reducing heat flux to a spacecraft during planetary re-entry. These ceramics contain tantalum disilicide, molybdenum disilicide and borosilicate glass. The components are milled, along with a processing aid, then applied to a surface of a porous substrate, such as a fibrous silica or carbon substrate. Following application, the coating is then sintered on the substrate. The composite structure is substantially impervious to hot gas penetration and capable of surviving high heat fluxes at temperatures approaching 3000.degree. F. and above.

Stewart, David A.↗

Analytic corrections to CFD heating predictions accounting for changes in surface catalysis

Integral boundary-layer solution techniques applicable to the problem of determining aerodynamic heating rates of hypersonic vehicles in the vicinity of stagnation points and windward centerlines are briefly summarized. A new approach for combining the insight afforded by integral boundary-layer analysis with comprehensive (but time intensive) computational fluid dynamic (CFD) flowfield solutions of the thin-layer Navier-Stokes equations is described. The approach extracts CFD derived quantities at the wall and at the boundary layer edge for inclusion in a post-processing boundary-layer analysis. It allows a designer at a workstation to address two questions, given a single CFD solution. (1) How much does the heating change for a thermal protection system with different catalytic properties than was used in the original CFD solution? (2) How does the heating change at the interface of two different TPS materials with an abrupt change in catalytic efficiency? The answer to the second question is particularly important, because abrupt changes from low to high catalytic efficiency can lead to localized increase in heating which exceeds the usually conservative estimate provided by a fully catalytic wall assumption.

Gnoffo, Peter A.↗

Analytic Corrections to CFD Heating Predictions Accounting for Changes in Surface Catalysis

A new approach for combining the insight afforded by integral boundary-layer analysis with comprehensive (but time intensive) computational fluid dynamic (CFD) flowfield solutions of the thin-layer Navier-Stokes equations is described. The approach extracts CFD derived quantities at the wall and at the boundary layer edge for inclusion in a post-processing boundary-layer analysis. It allows a designer at a work-station to address two questions, given a single CFD solution. (1) How much does the heating change for a thermal protection system (TPS) with different catalytic properties than was used in the original CFD solution? (2) How does the heating change at the interface of two different TPS materials with an abrupt change in catalytic efficiency? The answer to the second question is particularly important, because abrupt changes from low to high catalytic efficiency can lead to localized increase in heating which exceeds the usually conservative estimate provided by a fully catalytic wall assumption. Capabilities of this approach for application to Reusable Launch Vehicle (RLV) design are demonstrated. If the definition of surface catalysis is uncertain early in the design process, results show that fully catalytic wall boundary conditions provide the best baseline for CFD design points.

Gnoffo, Peter A.↗

Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (K i of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.

Science & Technology - Other Topics↗

Plasma-assisted manipulation of vanadia nanoclusters for efficient selective catalytic reduction of NO x

Supported nanoclusters (SNCs) with distinct geometric and electronic structures have garnered significant attention in the field of heterogeneous catalysis. However, their directed synthesis remains a challenge due to limited efficient approaches. This study presents a plasma-assisted treatment strategy to achieve supported metal oxide nanoclusters from a rapid transformation of monomeric dispersed metal oxides. As a case study, oligomeric vanadia-dominated surface sites were derived from the classic supported V 2 O 5 -WO 3 /TiO 2 (VWT) catalyst and showed nearly an order of magnitude increase in turnover frequency (TOF) value via an H 2 -plasma treatment for selective catalytic reduction of NO with NH 3 . Such oligomeric surface VO x sites were not only successfully observed and firstly distinguished from WO x and TiO 2 by advanced electron microscopy, but also facilitated the generation of surface amide and nitrates intermediates that enable barrier-less steps in the SCR reaction as observed by modulation excitation spectroscopy technologies and predicted DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

RNA-Cleaving DNA Enzymes with Altered Regio- or Enantioselectivity

In vitro evolution methods were used to obtain DNA enzymes that cleave either a 2',5' - phosphodiester following a wibonucleotide or a 3',5' -phosphodiester following an L-ribonucleotide. Both enzymes can operate in an intermolecular reaction format with multiple turnover. The DNA enzyme that cleaves a 2',5' -phosphodiester exhibits a k(sub cat) of approx. 0.01/ min and catalytic efficiency, k(sub cat)/k(sub m) of approx. 10(exp 5)/ M min. The enzyme that cleaves an L-ribonudeotide is about 10-fold slower and has a catalytic efficiency of approx. 4 x 10(exp 5)/ M min. Both enzymes require a divalent metal cation for their activity and have optimal catalytic rate at pH 7-8 and 35-50 C. In a comparison of each enzyme s activity with either its corresponding substrate that contains an unnatural ribonudeotide or a substrate that instead contains a standard ribonucleotide, the 2',5' -phosphodiester-deaving DNA enzyme exhibited a regioselectivity of 6000- fold, while the L-ribonucleotide-cleaving DNA enzyme exhibited an enantioselectivity of 50-fold. These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds.

Ordoukhanian, Phillip↗

Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities

Abstract Developing tunable and stable peroxidase mimetics with high catalytic efficiency provides a promising opportunity to improve and expand enzymatic catalysis in lignin depolymerization. A class of peptoid-based peroxidase mimetics with tunable catalytic activity and high stability is developed by constructing peptoids and hemins into self-assembled crystalline nanomaterials. By varying peptoid side chain chemistry to tailor the microenvironment of active sites, these self-assembled peptoid/hemin nanomaterials (Pep/hemin) exhibit highly modulable catalytic activities toward two lignin model substrates 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 3,3’,5,5’-tetramethylbenzidine. Among them, a Pep/hemin complex containing the pyridyl side chain showed the best catalytic efficiency ( V max / K m = 5.81 × 10 −3 s −1 ). These Pep/hemin catalysts are highly stable; kinetics studies suggest that they follow a peroxidase-like mechanism. Moreover, they exhibit a high efficacy on depolymerization of a biorefinery lignin. Because Pep/hemin catalysts are highly robust and tunable, we expect that they offer tremendous opportunities for lignin valorization to high value products.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and Biochemical Characterization of a Novel Hormone-Sensitive Lipase Family Esterase Est19 from the Antarctic Bacterium Pseudomonas sp. E2-15

Esterases represent an important class of enzymes with a wide variety of industrial applications. A novel hormone-sensitive lipase (HSL) family esterase, Est19, from the Antarctic bacterium Pseudomonas sp. E2-15 is identified, cloned, and expressed. The enzyme possesses a GESAG motif containing an active serine (S) located within a highly conserved catalytic triad of Ser 155 , Asp 253 , and His 282 residues. The catalytic efficiency (k cat /K m ) of Est19 for the pNPC6 substrate is 148.68 s –1 mM –1 at 40 °C. Replacing Glu 154 juxtaposed to the critical catalytic serine with Asp (E154→D substitution) reduced the activity and catalytic efficiency of the enzyme two-fold, with little change in the substrate affinity. The wild-type enzyme retained near complete activity over a temperature range of 10–60 °C, while ~50% of its activity was retained at 0 °C. A phylogenetic analysis suggested that Est19 and its homologs may represent a new subfamily of HSL. The thermal stability and stereo-specificity suggest that the Est19 esterase may be useful for cold and chiral catalyses.

59 BASIC BIOLOGICAL SCIENCES↗

Dual Enhancement of Thermostability and Activity of Xylanase through Computer-Aided Rational Design

In the realm of enzyme engineering, the dual enhancement of thermostability and activity remains a challenge. Herein, we employed a computer-aided approach integrating folding free energy calculations and evolutionary analysis to engineer Paecilomyces thermophila xylanase into a hyperthermophilic enzyme for application in the paper and pulp industry. Through the computational rational design, XynM9 with superior thermostability and enhanced activity was designed. Its optimal reaction temperature increases by 10 °C to 85 °C, its T m increases by 10 °C to 93 °C, and its half-life increases 11-fold to 5.8 h. Additionally, its catalytic efficiency improves by 57% to 3926 s –1 mM –1 . Molecular dynamics simulations revealed that XynM9 is stabilized by more hydrogen bonds and salt bridges than wild-type xylanase. The mutant’s narrower catalytic cleft enhances the substrate-binding affinity, thus improving the catalytic efficiency. In harsh conditions at 80 °C and pH 10, using XynM9 significantly reduced both hemicellulose and lignin, which makes it a good candidate for use in the paper and pulp process. Finally, our study presents an accurate and efficient strategy for the dual enhancement of enzyme properties, guiding further improvement of computational tools for protein stabilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Orbiter catalytic/noncatalytic heat transfer as evidenced by heating to contaminated surfaces on STS-2 and STS-3

During that portion of Space Shuttle orbiter entry when significant aerodynamic heat transfer occurs, the flow over the vehicle is in chemical nonequilibrium. The parameter which most significantly influences the level of surface heat transfer in such a flow field is the catalytic efficiency of the surface with respect to the recombination of dissociated oxygen atoms. Significant, and instantaneous, changes were observed in the level of heat transfer at several lower surface centerline locations on STS-2 and STS-3. This phenomenon apparently resulted from a sudden change in the surface catalytic efficiency at these locations due to contamination of the surface by metallic oxides. As a result, data obtained from affected measurements cannot be considered as benchmark data with which to attempt to characterize nonequilibrium heat transfer to the orbiter's lower surface centerline.

Throckmorton, D. A.↗

In vitro evolution of a ribozyme that contains 5-bromouridine

The Tetrahymena group I ribozyme was modified by replacing all 99 component uridine residues with 5-bromouridine. This resulted in a 13-fold reduction in catalytic efficiency in the RNA-catalyzed phosphoester-transfer reaction compared to the behavior of the unmodified ribozyme. A population of 10(13) variant ribozymes was constructed, each containing 5-bromouridine in place of uridine. Five successive 'generations' of in vitro evolution were carried out, selecting for improved phosphoester transferase activity. The evolved molecules exhibited a 27-fold increase in catalytic efficiency compared to the wild-type bromouridine-containing ribozyme, even exceeding that of the wild-type ribozyme in the non-brominated form. Three specific mutations were found to be responsible for this altered behavior. These mutations enhanced activity in the context of 5-bromouridine, but were detrimental in the context of unmodified uridine. The evolved RNAs not only tolerated but came to exploit the presence of the nucleotide analogue in carrying out their catalytic function.

NASA Discipline Exobiology↗

Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, operating independently from the host metabolism with reduced engineering complexity and improved theoretical yields. However, a major bottleneck was identified as the suboptimal kinetics of the core C1–C1 condensation enzyme, 2-hydroxyacyl-CoA synthase (HACS), catalyzing the acyloin condensation reaction between formaldehyde and formyl-CoA. Furthermore, we used a combinatorial approach of bioprospecting and rational protein engineering to identify multiple HACS variants with significantly improved activities toward C1 substrates. Sequence and structure alignment of the active variants elucidated the key regions for the catalytic function, which were targeted for mutagenesis, leading to improved catalytic efficiency. In parallel, a consecutive round of bioprospecting for homologs with high similarity with active variants revealed a highly active HACS variant exhibiting up to 7-fold improvement in catalytic efficiency (k cat /K M ) and 14-fold improvement in the FORCE pathway flux in vivo compared to the previous reports. Upon further optimization of the downstream pathway, the orthogonal C1-to-product bioconversion system showed a metabolic flux of up to 700 μM glycolate OD –1 h –1 (2.1 mmol gDCW –1 h –1 ) and an industrially relevant glycolate titer, rate, and yield of 5.2 g L –1 (67.8 mM), 0.22 g L –1 h –1 , and 94% carbon yield, respectively.

2-hydroxyacyl-CoA synthase↗

How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

Two steps forward—now look back Whether designed computationally or uncovered in activity screening, enzymes repurposed for biocatalysis rarely start at the peak of proficiency. However, directed evolution can in some cases increase catalytic efficiency of a poor enzyme by many orders of magnitude. Otten et al. used a suite of biochemical techniques to investigate the origins of rate enhancement in a previously evolved model enzyme. Two conformational states are present in the initial, computationally designed enzyme, but only one is active. Shifting the population toward the active state is one factor in increasing catalytic efficiency during evolution. Single mutations do not greatly increase activity, but the synergistic combination of just two out of 17 substitutions can provide most of the rate enhancement seen in the final, evolved enzyme. Science , this issue p. 1442

Science & Technology - Other Topics↗

Hydrophobic pockets built in polymer micelles enhance the reactivity of Cu 2+ ions

We report the hydrophobicity-enhanced reactivity of Cu2+ ions as an ester hydrolase. Using a dipicolylamine (DPA) containing reversible addition–fragmentation chain transfer agent, the synthetic sequence, either hydrophobic or hydrophilic first in amphiphilic block copolymers of polystyrene-block-poly(N'N-dimethylacrylamide) (PS-b-PDMA), was varied to control the location of the binding motif, DPA, in the hydrophobic core or on the hydrated corona of polymer micelles. The hydrophobicity of Cu 2+ sites showed a significant impact (as large as 60 times more activity) on their catalytic efficiency towards ester hydrolase. With two different kinetic modes, including Michaelis–Menten and the reverse saturation kinetics models, the binding constant Kb of the substrates to Cu 2+ sites were quantitatively analyzed and we demonstrate that hydrophobicity favors the binding of the substrates to Cu2+ sites at polymer micelles with smaller sizes, however, K b decays exponentially with micellar diameters. Despite the diffusion barrier, hydrophobicity shows a profound impact on the catalytic rate constant kc that measures the single conversion rate of bound substrates to products. There is a 16–20 times kinetic enhancement in the hydrolase activity, completely endowed by the hydrophobic microenvironment of Cu 2+ sites compared to micelles with similar sizes. Our results indicate how the hydrophobicity of Cu 2+ -containing micelles can impact the catalytic efficiency and potentially illustrate a promising way toward the design of bioinspired catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/ Q 10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity ( V max ) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. V max and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/ Q 10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.

59 BASIC BIOLOGICAL SCIENCES↗

Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase

Abstract Carbonic Anhydrases (CAs) have been a target forde novoprotein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes’ first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d 7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H 2 O/OH − )] N (TRIL2WL23H) 3 n+ that behaves similarly to native Co(II) substituted human‐CAs. Like the Zn(II) analogue, the cobalt‐derivative at slightly basic pH is incapable of hydrolyzing p‐nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH − )] N (TRIL2WL23H) 3 + peptide complex. X‐ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5‐coordinate species by pH 11. UV‐vis spectroscopy can monitor this transition, giving a pK a for the conversion of 10.3. We assign this conversion to the formation of a 5‐coordinate Co(II)(N imid ) 3 (OH)(H 2 O) species. The pH dependent kinetic analysis indicates the maximal rate (k cat ), and thus the catalytic efficiency (k cat /K m ), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.

Chemistry↗

A missense variant remote from the active site impairs stability of human phosphoglucomutase 1

Abstract Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease‐related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild‐type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. Synopsis Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.

Stiers, Kyle M.↗

Cobalt-Group 13 Complexes Catalyze CO 2 Hydrogenation via a Co(-I)/Co(I) Redox Cycle

The Co(-I) dihydrogen complexes, [(η 2 -H 2 )CoML]-, where ML is the group 13 metalloligand, N(o-(NCH 2 PiPr 2 )C 6 H 4 ) 3 M, and M is Al, Ga, or In, were previously reported ( J. Am. Chem. Soc. 2017, 139, 6570-6573). In this work, the related Co(-I) end-on dinitrogen adducts, [(N 2 )CoML]-, were isolated and investigated as precatalysts for CO 2 hydrogenation. The Co–Ga catalyst was highly active, achieving 19,200 formate turnovers with an initial turnover frequency of 27,000 h –1 under 34 atm of 1:1 CO 2 /H 2 and using Verkade’s proazaphosphatrane as a base at ambient temperature. The Co–Al catalyst was moderately active, while the Co–In complex was inactive. Hence, tuning the group 13 ion greatly influences the catalytic activity at the Co site. To elucidate the role of the group 13 support, experimental and theoretical mechanistic studies of the Co–Ga and Co–Al catalysts were conducted. The Co(-I) H 2 species are potent hydride donors with estimated thermodynamic hydricities (ΔG° H– ) of 32.0(1) and 37.4(1) kcal/mol in CH 3 CN for M = Al and Ga, respectively. By acting as masked Co(I) dihydrides, the Co(-I) H 2 species operate via an unusual Co(-I)/Co(I) redox cycle. After hydride transfer to CO 2 , the resulting intermediate is the Co(I) hydride complex, HCoML, which was independently synthesized and structurally characterized for M = Al and Ga. The Gibbs free energy for H 2 binding, ΔG° bind (1 atm), to generate (η 2 -H 2 )HCoML was slightly more favorable for HCoGaL (-4.2(1) kcal/mol) than for HCoAlL (-2.7(1) kcal/mol). In the subsequent step, the deprotonation reaction to regenerate the initial catalyst was much more favorable for (η 2 -H 2 )HCoGaL (pK a of 31.4, CH 3 CN) than for (η 2 -H 2 )HCoAlL (pK a of 34.3). Finally, the straightforward substitution of Al with Ga perturbs the energy profile of the catalytic reaction (|ΔΔG° H– | = 5.4 kcal/mol, |ΔΔG° bind | = 1.5 kcal/mol, and |ΔΔG° K a | = 4.0 kcal/mol) and thus provides a thermodynamic rationale for the higher catalytic efficiency of Co–Ga over Co–Al.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗