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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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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Polyketide synthase–like functionality acquired by plant fatty acid elongase

Fatty acid elongation typically proceeds through a four-step cycle of condensation, reduction, dehydration, and reduction for each two-carbon extension. Here, we describe a variation of this pathway in Orychophragmus limprichtianus, whose seed oil contains previously unknown C24-C28 keto-hydroxy fatty acids that account for ~25% of total fatty acids. These compounds are produced through an endoplasmic reticulum–localized discontinuous elongation process in which a 3-keto-hydroxy intermediate bypasses full reduction and is extended through a polyketide synthase–like mechanism. Transcriptomic and functional assays identified two divergent enzymes, a variant fatty acid elongase 1 (FAE1) and a low-activity 3-ketoacyl-CoA reductase (KCR1), as central to this process. Protein modeling and mutant analysis suggest that specific amino acid substitutions underlie altered KCR1 activity, enabling accumulation of keto intermediates. Our findings reveal unexpected flexibility in plant fatty acid elongation and provide innovative tools for engineering plants and microbes to produce renewable oils with tailored industrial functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Sulfonamidoboronic Acids as “Cross-Class” Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative organism listed as an urgent threat pathogen by the World Health Organization (WHO). Carbapenem-resistant A. baumannii (CRAB), especially, present therapeutic challenges due to complex mechanisms of resistance to β-lactams. One of the most important mechanisms is the production of β-lactamase enzymes capable of hydrolyzing β-lactam antibiotics. Co-expression of multiple classes of β-lactamases is present in CRAB; therefore, the design and synthesis of “cross-class” inhibitors is an important strategy to preserve the efficacy of currently available antibiotics. To identify new, nonclassical β-lactamase inhibitors, we previously identified a sulfonamidomethaneboronic acid CR167 active against Acinetobacter-derived class C β-lactamases (ADC-7). The compound demonstrated affinity for ADC-7 with a K i = 160 nM and proved to be able to decrease MIC values of ceftazidime and cefotaxime in different bacterial strains. Herein, we describe the activity of CR167 against other β-lactamases in A. baumannii: the cefepime-hydrolysing class C extended-spectrum β-lactamase (ESAC) ADC-33 and the carbapenem-hydrolyzing OXA-24/40 (class D). These investigations demonstrate CR167 as a valuable cross-class (C and D) inhibitor, and the paper describes our attempts to further improve its activity. Five chiral analogues of CR167 were rationally designed and synthesized. The structures of OXA-24/40 and ADC-33 in complex with CR167 and select chiral analogues were obtained. The structure activity relationships (SARs) are highlighted, offering insights into the main determinants for cross-class C/D inhibitors and impetus for novel drug design.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Leafweb: Leaf Gas Exchange and Pulse-Amplitude Modulated Fluorometry for C4 Species, June 2026 Release

This dataset contains leaf gas exchange and Pulse-Amplitude Modulated (PAM) fluorometry for 98 C4 species. The C4 photosynthetic pathway employs specialized CO2 concentration mechanisms and Kranz anatomy to enrich CO2 concentration around Rubisco, the enzyme that catalyzes carbon fixation in the Calvin-Benson cycle to suppress photorespiration and increase the use efficiencies of light, nitrogen, and water as compared to the C3 photosynthetic pathways. Large-scale C4 photosynthetic datasets are relatively scarce, which has affected C4 photosynthesis research. To improve C4 photosynthetic data availability, Leafweb organized an effort to systematically collect, compile, standardize, and organize measurements of leaf gas exchange and/or Pulse-Amplitude Modulated (PAM) fluorometry of C4 species. This derived a C4 photosynthetic dataset containing measurements made by independent researchers in multiple countries in various environments (field, garden, or greenhouse). It covers three biochemical subtypes – the nicotinamide adenine dinucleotide phosphate-malic enzyme (NADP-ME), nicotinamide adenine dinucleotide-malic enzyme (NAD-ME), and phosphoenolpyruvate carboxykinase (PEP-CK) subtypes. This dataset is useful for using Artificial Intelligence / Machine Learning and mechanistic models to study C4 photosynthesis and compare across different biochemical subtypes. This dataset contains 3 compressed (*.zip) folders containing 1,892 data files in comma-separate values (*.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma-separate values (*.csv) format and a user guide in PDF (*.pdf) format.

Zhou, Haoran [Tianjin University, China]↗
DOE OSTI2022

Allosteric control of electron transfer in nitrogenase and nitrogenase-like enzymes (Final Report)

More than a third of all known proteins to date are either oxidoreductases or metalloproteins. The diversity of metal cofactors and redox centers in these proteins make them attractive candidates for engineering protein-based biocatalysts, biosensors, and biofuel cells, among other necessary tools for the bioeconomy. Many of these enzymes function as large multi-subunit complexes arranged as symmetric or asymmetric assemblies, and the purpose of this architecture is unclear. The goal of the project was to address this fundamental question by investigating the mechanism of action of two oxidoreductases: Nitrogenase and DPOR (Dark-Operative Protochlorophyllide Oxidoreductase, a nitrogenase-like oxidoreductase). Nitrogenase and DPOR play key roles in nitrogen fixation and photosynthesis, processes essential to sustaining life. Both proteins are arranged as two symmetrical halves with each half capable of substrate reduction. For more than half a century, substrate reduction by nitrogenase has been presumed to occur independently within the two identical halves. Funded by this DOE grant we have now shown that both nitrogenase and DPOR function asymmetrically. Electron transfer in one half suppresses activity in the other. Thus, we have demonstrated that the two halves do not function in an independent manner; rather, catalytic events in one-half allosterically suppress activity and electron transfer (ET) in the other. This alternating-site mechanism has significant implications on our current understanding of substrate reduction by these enzymes and offers a new mechanistic paradigm for the reactions they catalyze. Our work now provides a mechanistic map of the how the two symmetric catalytic halves work together to establish and maintain the sequential-site mechanism through multiple ET cycles to achieve substrate reduction. There is substantive need for bio-inspired tools that enable reduction of nitrogen and other substrates, as well as photosynthesis, for energy and food production. Understanding the workings of enzymes like nitrogenase and DPOR that mediate multi-electron redox chemistry is vital for designing such synthetic tools. The timing of our research coincides with the biotechnological breakthrough of light-driven artificial N2 reduction by nitrogenase, achieved using the native enzyme with both halves arranged in a mirror-like architecture as catalyst. Together with such discoveries, our research now reveal unknown facets of the reaction mechanism and hold promise for designing more effective catalysts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Post-translational Histidine–Histidine Cross-Link Enhances Enzymatic Oxygen Reduction Activity with Greater pH Adaptability

Cross-linked protein residues exist as enzyme cofactors to enable or enhance catalytic activities. Despite their importance in nature, the chemical identity of the cross-links is limited to certain amino acid combinations, whose function and the formation mechanism remain insufficiently understood due to the difficulty in isolating native enzymes without the cross-links. Herein, we report the formation and characterization of both His-Tyr and His-His cross-links under oxidative enzymatic turnover conditions in L29H/F33Y/F43H Mb, a structural and functional model of heme-copper oxidase (HCO). The connectivity of the cross-link was characterized as Ne ε2 (His29)-Cd δ2 (His43) by mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR). Interestingly, formation of the cross-link significantly enhances the oxygen reduction activity of the enzyme at neutral or basic pH with higher product specificity. X-ray crystallography has identified a novel Tyr-His cross-link through a Tyr-O-His linkage. Our mechanistic studies indicate the involvement of high-valent heme-iron and the neighboring tyrosine in an oxidative self-processing pathway to generate the cross-link. In conclusion, this work serves as a new example while providing insights into the enzyme cross-link formation, allowing the design of artificial biocatalysts containing these novel cross-links with higher activity and pH adaptability.

Liu, Yiwei [Univ. of Texas, Austin, TX (United Sta↗
DOE OSTI2021

The moderately defficient enzyme: Catalysis-related damage in vivo and its repair

Enzymes have in vivo lifespans. Analysis of lifespans – lifetime totals of catalytic turnovers – suggests that non-survivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme lifespan might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements is lacking: there are too few measurements of in vivo lifespan, and existing information on the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach to identify, predict, and validate instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability, and could change thinking about which enzymes die young in vivo, and why.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The moderately defficient enzyme: Catalysis-related damage in vivo and its repair

Enzymes have in vivo lifespans. Analysis of lifespans – lifetime totals of catalytic turnovers – suggests that non-survivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme lifespan might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements is lacking: there are too few measurements of in vivo lifespan, and existing information on the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach to identify, predict, and validate instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability, and could change thinking about which enzymes die young in vivo, and why.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Influence of cellular redox reactions on the structure and function of light harvesting and photosystems

Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair

Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Melt Processing Pretreatment Effects on Enzymatic Depolymerization of Poly(ethylene terephthalate)

Poly(ethylene terephthalate) (PET) is a common thermoplastic material, used in a wide variety of applications (i.e., bottles, fabrics, packaging, electronics, and automotive components). Increasing demand for PET has precipitated a need for improved recycling technology, especially for single-use PET waste. Recently, enzymatic depolymerization has shown promise as an environmentally responsible alternative for PET chemical recycling that yields economically useful products (e.g., terephthalic acid, adipic acid, and ethylene glycol). However, the depolymerization system still suffers from low rates on crystalline PET substrates, and effects of realistic waste streams are not known. In our work, PET waste is pretreated using an ultra-high-speed twin-screw extruder system. PET substrates were modified by various processing pretreatments to allow enzymes better access to depolymerize substrate materials. The effect of varying throughput and mechanical shear on structural properties of the PET waste was analyzed using molecular weight and thermal characterizations. These pretreated samples exhibit modifications in molecular weight, glass transition temperature, crystallinity, and specific surface area. The unpurified leaf-branch compost cutinase enzyme produced from the fed-batch fermentation of Escherichia coli BL21(DE3) was used in enzymatic depolymerization, where a faster reaction was observed as crystallinity was decreased and the specific surface area was increased. The rate of terephthalic acid production was also significantly higher for samples processed at lower mechanical shear with higher throughputs. As a result, this work demonstrates the potential for tailoring pretreatments in pursuit of faster and more energy efficient PET recycling using enzymes, with facile adaptation to the industrial scale for the circular economy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Switchable client specificity in a dual functional chaperone coordinates light-harvesting complex biogenesis

The proper assembly of light-harvesting complexes (LHCs) is critical for photosynthesis and requires the biogenesis of light-harvesting chlorophylla,b-binding proteins (LHCPs) to be coordinated with chlorophyll (Chl) biosynthesis. The mechanism underlying this coordination is not well understood. Here, we show that a conserved molecular chaperone, chloroplast signal recognition particle 43-kDa protein (cpSRP43), provides a molecular thermostat that helps maintain this coordination. cpSRP43 undergoes a conformational rearrangement between a well-folded closed state and a partially disordered open state. Closed cpSRP43 is dedicated to the biogenesis of LHCPs, whereas open cpSRP43 protects multiple Chl biosynthesis enzymes from heat-induced destabilization. Rising temperature shifts cpSRP43 to the open state, enabling it to protect heat-destabilized Chl biosynthesis enzymes. Our results reveal the molecular basis of a posttranslational mechanism for the thermoadaptation of LHC biogenesis. They also demonstrate how an adenosine triphosphate–independent chaperone uses conformational dynamics to switch its activity and client selectivity, thereby adapting to different proteostatic demands under shifting environmental conditions.

Science & Technology - Other Topics↗
DOE OSTI2021

Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more than 90% loss of activity of the wild-type G6PD. The crystal structure of G6PD reveals these mutations are located away from the active site, concentrating around the noncatalytic NADP + -binding site and the dimer interface. However, the molecular mechanisms of class I mutant dysfunction have remained elusive, hindering the development of efficient therapies. To resolve this, we performed integral structural characterization of five G6PD mutants, including four class I mutants, associated with the noncatalytic NADP + and dimerization, using crystallography, small-angle X-ray scattering (SAXS), cryogenic electron microscopy (cryo-EM), and biophysical analyses. Comparisons with the structure and properties of the wild-type enzyme, together with molecular dynamics simulations, bring forward a universal mechanism for this severe G6PD deficiency due to the class I mutations. We highlight the role of the noncatalytic NADP + -binding site that is crucial for stabilization and ordering two β-strands in the dimer interface, which together communicate these distant structural aberrations to the active site through a network of additional interactions. This understanding elucidates potential paths for drug development targeting G6PD deficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular “reactors.” In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chlorophyllase from Arabidopsis thaliana Reveals an Emerging Model for Controlling Chlorophyll Hydrolysis

Chlorophyll (Chl) is one of Nature’s most complex pigments to biosynthesize and derivatize. This pigment is vital for survival and also paradoxically toxic if overproduced or released from a protective protein scaffold. Therefore, along with the mass production of Chl, organisms also invest in mechanisms to control its degradation and recycling. One important enzyme that is involved in these latter processes is chlorophyllase. This enzyme is employed by numerous photosynthetic organisms to hydrolyze the phytol tail of Chl. Although traditionally thought to catalyze the first step of Chl degradation, recent work suggests that chlorophyllase is instead employed during times of abiotic stress or conditions that produce reactive oxygen species. However, the molecular details regarding how chlorophyllases are regulated to function under such conditions remain enigmatic. Here, we investigate the Arabidopsis thaliana chlorophyllase isoform AtCLH2 using site-directed mutagenesis, mass spectrometry, dynamic light scattering, size-exclusion multiangle light scattering, and both steady-state enzyme kinetic and thermal stability measurements. Through these experiments, we show that AtCLH2 exists as a monomer in solution and contains two disulfide bonds. One disulfide bond putatively maps to the active site, whereas the other links two N-terminal Cys residues together. These disulfide bonds are cleaved by chemical or chemical and protein-based reductants, respectively, and are integral to maintaining the activity, stability, and substrate scope of the enzyme. This work suggests that Cys residue oxidation in chlorophyllases is an emerging regulatory strategy for controlling the hydrolysis of Chl pigments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dynamics of Rubisco regulation by sugar phosphate derivatives and their phosphatases

Regulating the central CO 2 -fixing enzyme Rubisco is as complex as its ancient reaction mechanism and involves interaction with a series of cofactors and auxiliary proteins that activate catalytic sites and maintain activity. A key component among the regulatory mechanisms is the binding of sugar phosphate derivatives that inhibit activity. Removal of inhibitors via the action of Rubisco activase is required to restore catalytic competency. In addition, specific phosphatases dephosphorylate newly released inhibitors, rendering them incapable of binding to Rubisco catalytic sites. The best studied inhibitor is 2-carboxy-d-arabinitol 1-phosphate (CA1P), a naturally occurring nocturnal inhibitor that accumulates in most species during darkness and low light, progressively binding to Rubisco. As light increases, Rubisco activase removes CA1P from Rubisco, and the specific phosphatase CA1Pase dephosphorylates CA1P to CA, which cannot bind Rubisco. Misfire products of Rubisco’s complex reaction chemistry can also act as inhibitors. One example is xylulose-1,5-bisphosphate (XuBP), which is dephosphorylated by XuBPase. Here we revisit key findings related to sugar phosphate derivatives and their specific phosphatases, highlighting outstanding questions and how further consideration of these inhibitors and their role is important for better understanding the regulation of carbon assimilation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O 2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Utilization of protein film electrochemistry to characterize the mechanisms imparting aerotolerance and bidirectionality in soluble, multimeric [NiFe]-hydrogenases (Final Report for Grant No. DE-SC0008074)

The overall goal of this project was to better understand how structural features control functional aspects of enzymes involved in catalysis in which a substrate is oxidized or reduced. Two types of model enzymes were explored: the soluble [NiFe]-hydrogenase from Pyrococcus furiousus and the thiosulfate reductase from Pyrobaculum aerophilum. Both are models for complex, multielectron transformations such as nitrogen and carbon dioxide reduction, and parts of important biogeochemical cycles. In this project, electrochemical methods were used to define the activities of these enzymes and targeted variants designed to modulate activity. We showed that the catalytic activity of the soluble hydrogenase from Pyrococcus furiosus can be modulated by removing large parts of the enzyme far from the active site. This surprising result suggests that interactions between functional centers far apart within the enzyme may be essential for controlling and tuning activity. We also showed that the catalytic activity of thiosulfate reductase from Pyrobaculum aerophilum can be modulated by changing the metal at the active site to be either molybdenum or tungsten. These results contribute to our understanding of how the protein environment can tune the reactivity of an embedded metal, catalytic center. The results were and are being published in peer-reviewed, scientific publications.

08 HYDROGEN↗