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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Spectral deconvolution of redox species in the crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from Megasphaera elsdenii. A flavin-dependent bifurcating enzyme
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Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase
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Mycobacterium tuberculosis Exploits a Heterohexameric Enoyl-CoA Hydratase Retro-Aldolase Complex for Cholesterol Catabolism
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Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO 2 and CO Fixation
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Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele
Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(–/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(–/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(–/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(–/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(–/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Furthermore, our findings open up new possibilities for stably fine-tuning residual gene function in planta.
Discovery and mechanism of a highly selective, antifungal acetyl-CoA synthetase inhibitor
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Site specific redox properties in ligand differentiated di-nickel complexes inspired by the acetyl CoA synthase active site
These complexes, comprised of Ni(N 2 S 2 )–Ni(dithiolene) S-bridged units, serve as a platform to interrogate the positions of added electrons. Tuning of the ligand substituents controls electron uptake in S-bridged dinickel complexes.
The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the
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Subunit specificity of the two acetyl-CoA synthetases of yeast as revealed by an immunological approach
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Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis
Family 1 Coenzyme A transferases (CtfAB) from the extremely thermophilic bacterium, Thermosipho melanesiensis, has been used for in vivo acetone production up to 70°C. This enzyme has tentatively been identified as the rate-limiting step, due to its relatively low-binding affinity for acetate. However, existing kinetic and mechanistic studies on this enzyme are insufficient to evaluate this hypothesis. Here, kinetic analysis of purified recombinant T. melanesiensis CtfAB showed that it has a ping-pong bi-bi mechanism typical of Coenzyme A (CoA) transferases with Km values for acetate and acetoacetyl-CoA of 85 mM and 135 μM, respectively. Product inhibition by acetyl-CoA was competitive with respect to acetoacetyl-CoA and non-competitive with respect to acetate. Crystal structures of wild-type and mutant T. melanesiensis CtfAB were solved in the presence of acetate and in the presence or absence of acetyl-CoA. These structures led to a proposed structural basis for the competitive and non-competitive inhibition of acetyl-CoA: acetate binds independently of acetyl-CoA in an apparent low-affinity binding pocket in CtfA that is directly adjacent to a catalytic glutamate in CtfB. Similar to other CoA transferases, acetyl-CoA is bound in an apparent high-affinity binding site in CtfB with most interactions occurring between the phospho-ADP of CoA and CtfB residues far from the acetate binding pocket. This structural-based mechanism also explains the organic acid promiscuity of CtfAB. High-affinity interactions are predominantly between the conserved phospho-ADP of CoA, and the variable organic acid binding site is a low-affinity binding site with few specific interactions.
A Generalized Nuclear Code of Accounts for Cost Estimation Standardization
This is a joint INL-EPRI study. Link to corresponding page at the Electric Power Research Institute (EPRI): https://www.epri.com/research/products/000000003002028937 Recent Advanced Reactor (AR) designs typically offer features and attributes that depart from traditional water-cooled reactors in terms of fuel forms, coolants, structural materials, size, safety margins, and other important design and operational aspects. These departures, relative to the industry experience, will likely present a challenge for potential owner-operators when evaluating one or more AR designs for commercial deployment on a like-for-like basis. This is further exacerbated with new classes of reactors gaining prominence (e.g., microreactors) and new emerging applications (e.g., floating barge reactors or space propulsion reactors). The differences in design-specific technologies are compounded by the differences in approach to cost estimation. The lack of consistency in build up toward cost estimates creates a challenge when comparing competing concepts and evaluating their associated cost drivers. The outcome of a 2019 Scoping Study conducted by the Electric Power Research Institute (EPRI) indicated the need for a cost modeling guide (CMG), which would be underpinned by a technology-neutral and inclusive Generalized Nuclear Code of Accounts (GN-COA). A code of accounts (COA) is a tool by which costs are identified in even more specific categories, providing clarity on what specific costs are included in an estimate. A parallel independent effort was meanwhile taking place at Idaho National Laboratory via funding by the Systems Analysis Integration (SA&I) campaign of the Office of Nuclear Energy under the U.S. Department of Energy (U.S. DOE-NE) to also update the COA structure to enable more flexibility and encompass a wider variety of reactor technologies. After being made aware of these synergistic efforts, the two parties decided to combine efforts and develop a joint new standard format for nuclear cost estimation that builds on previous structures. This document describes the development of this joint GN-COA and provides guidance on the implementation of the tool, which is provided as the associated GN-COA Excel document. The main attributes of this novel COA format are that all items are functionally defined (in order to be technology and application agnostic) and grouped into logical arrangements that facilitate the tabulation of costs for reactor constructions under consideration. The intent is for the GN-COA to form a standard that is endorsed by future vendors and customers.
Holographic Weapons Sight as Crew Optical Alignment Sight
Crew Optical Alignment Sights (COAS) are used by spacecraft pilots to provide a visual reference to a target spacecraft for lateral relative position during rendezvous and docking operations. NASA s Orion vehicle, which is currently under development, has not included a COAS in favor of automated sensors, but the crew office has requested such a device be added for situational awareness and contingency support. The current Space Shuttle COAS was adopted from Apollo heritage, weighs several pounds, and is no longer available for procurement which would make re-use difficult. In response, a study was conducted to examine the possibility of converting a commercially available weapons sight to a COAS for the Orion spacecraft. The device used in this study was the XPS series Holographic Weapon Sight (HWS) procured from L-3 EOTech. This device was selected because the targeting reticule can subtend several degrees, and display a graphic pattern tailored to rendezvous and docking operations. Evaluations of the COAS were performed in both the Orion low-fidelity mockup and rendezvous simulations in the Reconfigurable Operational Cockpit (ROC) by crewmembers, rendezvous engineering experts, and flight controllers at Johnson Space Center. These evaluations determined that this unit s size and mounting options can support proper operation and that the reticule visual qualities are as good as or better than the current Space Shuttle COAS. The results positively indicate that the device could be used as a functional COAS and supports a low-cost technology conversion solution.
Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family
2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled the use of molecules derived from greenhouse gases as biomanufacturing feedstocks. We investigated several HACL/S family members with high activity in the condensation of formyl-CoA and aldehydes, and distinct chain-length specificities and kinetic parameters. Our analysis revealed the structures of enzymes in complex with acyl-CoA substrates and products, several covalent intermediates, bound ThDP and ADP, as well as the C-terminal active site region. One of these observed states corresponds to the intermediary α–carbanion with hydroxymethyl-CoA covalently attached to ThDP. This research distinguishes HACL/S from related sub-families and identifies key residues involved in substrate binding and catalysis. These findings expand our knowledge of acyloin-condensation biochemistry and offer attractive prospects for biocatalysis using carbon elongation.
New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions
Background: The great metabolic versatility of the purple non-sulfur bacteria is of particular interest in green technology. Rhodospirillum rubrum S1H is an α-proteobacterium that is capable of photoheterotrophic assimilation of volatile fatty acids (VFAs). Butyrate is one of the most abundant VFAs produced during fermentative biodegradation of crude organic wastes in various applications. While there is a growing understanding of the photoassimilation of acetate, another abundantly produced VFA, the mechanisms involved in the photoheterotrophic metabolism of butyrate remain poorly studied. Results: In this work, we used proteomic and functional genomic analyses to determine potential metabolic pathways involved in the photoassimilation of butyrate. We propose that a fraction of butyrate is converted to acetyl-CoA, a reaction shared with polyhydroxybutyrate metabolism, while the other fraction supplies the ethylmalonyl-CoA (EMC) pathway used as an anaplerotic pathway to replenish the TCA cycle. Surprisingly, we also highlighted a potential assimilation pathway, through isoleucine synthesis and degradation, allowing the conversion of acetyl-CoA to propionyl-CoA. We tentatively named this pathway the methylbutanoyl-CoA pathway (MBC). An increase in isoleucine abundance was observed during the early growth phase under butyrate condition. Nevertheless, while the EMC and MBC pathways appeared to be concomitantly used, a genome-wide mutant fitness assay highlighted the EMC pathway as the only pathway strictly required for the assimilation of butyrate. Conclusion: Photoheterotrophic growth of Rs. rubrum with butyrate as sole carbon source requires a functional EMC pathway. In addition, a new assimilation pathway involving isoleucine synthesis and degradation, named the methylbutanoyl-CoA (MBC) pathway, could also be involved in the assimilation of this volatile fatty acid by Rs. rubrum.
Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris
Abstract Rhodopseudomonas palustris is a model microorganism for studying the anaerobic metabolism of aromatic compounds. While it is well documented which aromatics can serve as sole organic carbon sources, co-metabolism of other aromatics is poorly understood. This study used kinetic modeling to analyze the simultaneous degradation of aromatic compounds present in corn stover hydrolysates and model the co-metabolism of aromatics not known to support growth of R. palustris as sole organic substrates. The simulation predicted that p -coumaroyl amide and feruloyl amide were hydrolyzed to p -coumaric acid and ferulic acid, respectively, and further transformed via p -coumaroyl-CoA and feruloyl-CoA. The modeling also suggested that metabolism of p -hydroxyphenyl aromatics was slowed by substrate inhibition, whereas the transformation of guaiacyl aromatics was inhibited by their p -hydroxyphenyl counterparts. It also predicted that substrate channeling may occur during degradation of p -coumaroyl-CoA and feruloyl-CoA, resulting in no detectable accumulation of p -hydroxybenzaldehyde and vanillin, during the transformation of these CoA ligated compounds to p- hydroxybenzoic acid and vanillic acid, respectively. While the simulation correctly represented the known transformation of p -hydroxybenzoic acid via the benzoyl-CoA pathway, it also suggested co-metabolism of vanillic acid and syringic acid, which are known not to serve as photoheterotrophic growth substrate for R. palustris .