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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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52 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Engineering a photoenzyme to use red light

Photoenzymatic reactions involving flavin-dependent “ene”-reductases (EREDs) rely on protein-templated charge transfer (CT) complexes between the cofactor and substrate for radical initiation. These complexes typically absorb in the blue region of the electromagnetic spectrum. Here, we engineered an ERED to form CT complexes that absorb red light. Mechanistic studies indicate that red-light activity is due to the growth of a red-absorbing shoulder off the previously identified cyan absorption feature. Molecular dynamics simulations, docking, and excited-state calculations suggest that the cyan feature involves a π→π* transition on flavin, whereas the red-light absorption is a π→π* transition between flavin and the substrate. Furthermore, differences in the electronic transition are due to changes in the substrate-binding conformation and allosteric tuning of the electronic structure of the cofactor-substrate complex. Microenvironment tuning of the CT complex for red-light activity is observed with other engineered photoenzymatic reactions, highlighting this effect’s generality.

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

Workflow for evaluating enzyme immobilization and performance for continuous flow manufacturing

Enzymes have shown promise in various industries due to their functional specificity, catalytic efficiency, and environmental sustainability. These biological catalysts can be a pivotal component of manufacturing pipelines like continuous flow chemistry. For this, there exists a need to robustly immobilize enzymes on solid supports and assess the effects of the solid supports on catalytic performance and stability. Here, we use an industrially relevant model enzyme, C. ensiformis (Jack bean) urease, to demonstrate immobilization and assess performance in the context of continuous flow manufacturing. Various immobilization strategies were screened focusing on immobilization efficiency, protocol simplicity, and urease biocatalyst kinetics. Based on this, CDI-agarose and NHS-agarose resins were identified as the best-performing immobilization strategies for urease. CDI-agarose-urease and NHS-agarose-urease were then scaled up and applied to a large-scale continuous flow reactor to evaluate product yields, operational stability, and long-term stability. These experiments identified differences in stability and performance depending on the immobilization method tested. This highlights the importance of screening immobilization methods and subsequent enzyme performance for each candidate biocatalyst used in manufacturing to promote optimal performance and stability. As such, this work provides a framework for evaluating enzyme biocatalyst immobilization approaches to improve performance and enable transition into industrial processes.

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

Red-Light-Driven Biophotochemical Diode Based on a Microorganism–Silicon Nanowire Interface for Stable and Efficient Bias-Free CO 2 Reduction

Artificial photosynthesis offers a promising route for sustainable liquid fuel and feedstock production, yet integrating efficient CO 2 reduction catalysts with light-harvesting systems remains challenging. Here, in this study, we present a biophotochemical diode that couples microorganism-driven CO 2 reduction with glycerol oxidation, enabled by silicon nanowire photoelectrodes under varying red-light intensities. Tuning the biotic-abiotic interface─by increasing biocatalyst loading and adjusting the catholyte pH to mitigate local alkalization─significantly improves performance and stability. The enhanced-loading biocathode maintains a high faradaic efficiency across a wide potential range, even under elevated light intensities. At 60 mW/cm 2 , the system achieves a bias-free current density of 3.5 mA/cm 2 . Long-term stability testing at 40 mW/cm 2 demonstrates stable operation for over 100 h. The photoanode generates valuable C 3 products, primarily glycerate and lactate, enhancing the economic viability. This work showcases the importance of microenvironmental control at the biotic-abiotic interface and establishes a scalable platform for light-driven CO 2 reduction using earth-abundant silicon.

Artificial Photosynthesis↗
DOE OSTI2024

Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst

Biological systems can directly upgrade carbon dioxide (CO 2 ) into chemicals. The CO 2 fixation rate of autotrophic organisms, however, is too slow for industrial utility, and the breadth of engineered metabolic pathways for the synthesis of value-added chemicals is too limited. Biotechnology workhorse organisms with extensively engineered metabolic pathways have recently been engineered for CO 2 fixation. Yet, their low carbon fixation rate, compounded by the fact that living organisms split their carbon between cell growth and chemical synthesis, has led to only cell growth with no chemical synthesis achieved to date. Here, we engineer a lysate-based cell-free expression (CFE)-based multienzyme biocatalyst for the carbon negative synthesis of the industrially relevant amino acids glycine and serine from CO 2 equivalents–formate and bicarbonate–and ammonia. The formate-to-serine biocatalyst leverages tetrahydrofolate (THF)-dependent formate fixation, reductive glycine synthesis, serine synthesis, and phosphite dehydrogenase-dependent NAD(P)H regeneration to convert 30% of formate into serine and glycine, surpassing the previous 22% conversion using a purified enzyme system. We find that (1) the CFE-based biocatalyst is active even after 200-fold dilution, enabling higher substrate loading and product synthesis without incurring additional cell lysate cost, (2) NAD(P)H regeneration is pivotal to driving forward reactions close to thermodynamic equilibrium, (3) balancing the ratio of the formate-to-serine pathway genes added to the CFE is key to improving amino acid synthesis, and (4) efficient THF recycling enables lowering the loading of this cofactor, reducing the cost of the CFE-based biocatalyst. To our knowledge, this is the first synthesis of amino acids that can capture CO 2 equivalents for the carbon negative synthesis of amino acids using a CFE-based biocatalyst. Looking ahead, the CFE-based biocatalyst process could be extended beyond serine to pyruvate, a key intermediate, to access a variety of chemicals from aromatics and terpenes to alcohols and polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Revisiting the activity of two poly(vinyl chloride)- and polyethylene-degrading enzymes

Biocatalytic degradation of non-hydrolyzable plastics is a rapidly growing field of research, driven by the global accumulation of waste. Enzymes capable of cleaving the carbon-carbon bonds in synthetic polymers are highly sought-after as they may provide tools for environmentally friendly plastic recycling. Despite some reports of oxidative enzymes acting on non-hydrolyzable plastics, including polyethylene or poly(vinyl chloride), the notion that these materials are susceptible to efficient enzymatic degradation remains controversial, partly driven by a general lack of studies independently reproducing previous observations. Here, we attempt to replicate two recent studies reporting that deconstruction of polyethylene and poly(vinyl chloride) can be achieved using an insect hexamerin from Galleria mellonella (so-called “Ceres”) or a bacterial catalase-peroxidase from Klebsiella sp., respectively. Reproducing previously described experiments, we do not observe any activity on plastics using multiple reaction conditions and multiple substrate types. Digging deeper into the discrepancies between the previous data and our observations, we show how and why the original experimental results may have been misinterpreted.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst

Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H 2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Sequence-based generative AI design of versatile tryptophan synthases

Enzymes are powerful and sustainable catalysts, but their widespread application is limited by the difficulty of identifying functional starting points for optimization, creating a major bottleneck in early- stage biocatalyst discovery. Designing libraries of such starting enzymes remains particularly challenging. Here, we use the GenSLM protein language model to generate novel β-subunit of tryptophan synthase (TrpB) enzymes that express in Escherichia coli and are both stable and catalytically active. Many generated TrpBs also display significant substrate promiscuity, outperforming their natural counterparts on non-native substrates. Some even surpass laboratory-evolved TrpBs. Comparison of the most-active and most-promiscuous generated TrpB to its closest natural homolog confirms that the enhanced versatility is absent from the natural enzyme, highlighting the creative potential of generative models. These results demonstrate that the generated TrpBs not only preserve natural structure and function but also acquire non-natural properties, establishing generative models as powerful tools for biocatalyst discovery and engineering.

biocatalysis↗
DOE OSTI2025

Copper-dependent halogenase catalyses unactivated C−H bond functionalization

Carbon–hydrogen (C–H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp 3 )−H bond. In recent years, metalloenzymes have been found to perform C(sp 3 )−H bond functionalization. Despite substantial progresses in the past two decades, enzymatic halogenation and pseudohalogenation of unactivated C(sp 3 )−H—providing a functional handle for further modification—have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes. Here, in this work, we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp 3 )−H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp 3 )−H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs—one interchain and two intrachain—of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp 3 )−H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

biocatalysis↗
DOE OSTI2024

A red-light-powered silicon nanowire biophotochemical diode for simultaneous CO 2 reduction and glycerol valorization

A bias-free photochemical diode, in which a p-type photocathode is connected to an n-type photoanode to harness light for driving photoelectrochemical reduction and oxidation pairs, serves as a platform for realizing light-driven fuel generation from CO 2 . However, the conventional design, in which cathodic CO 2 reduction is coupled with the anodic oxygen evolution reaction (OER), requires substantial energy input. Here we present a photochemical diode device that harnesses red light (740 nm) to simultaneously drive biophotocathodic CO 2 -to-multicarbon conversion and photoanodic glycerol oxidation as an alternative to the OER to overcome the above thermodynamic limitation. The device consists of an efficient CO 2 -fixing microorganism, Sporomusa ovata, interfaced with a silicon nanowire photocathode and a Pt–Au-loaded silicon nanowire photoanode. This photochemical diode operates bias-free under low-intensity (20 mW cm –2 ) red light irradiation with ~80% Faradaic efficiency for both the cathodic and anodic products. Finally, this work provides an alternative photosynthetic route to mitigate excessive CO 2 emissions and efficiently generate value-added chemicals from CO 2 and glycerol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Carbon conversion on biophotonic leaf

A photodiode can trigger bias-free redox reactions but is often hindered by thermodynamic barriers. Now, a bacteria-conjugated silicon biophotochemical diode allows simultaneous conversion of various carbon molecules with high efficacy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids

Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here we present an approach that uses a modular polyketide synthase (PKS) platform for the efficient production of these compounds. This platform takes advantage of a versatile loading module from the rimocidin PKS and nicotinamide adenine dinucleotide phosphate-dependent terminal thioreductases. Reduction of the terminal aldehyde with alcohol dehydrogenases enables the production of diols, oxidation enables the production of hydroxy acids and specific transaminases allow the production of various amino alcohols. Furthermore, replacement of the malonyl-coenzyme A-specific acyltransferase in the extension module with methyl- or ethylmalonyl-coenzyme A-specific acyltransferase enables the production of branched-chain diols, amino alcohols and carboxylic acids in high titres. Use of our PKS platform in Streptomyces albus demonstrated the high tunability and efficiency of the platform.

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

Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds

Bacteria utilize methylthio-alkane reductase (MAR) to acquire sulfur from volatile organic sulfur compounds. Reductive cleavage of methylthio-ethanol and dimethylsulfide liberates methanethiol for methionine synthesis and concomitantly releases ethylene and methane, respectively. Here we show that the native MAR of Rhodospirillum rubrum is a two-component system composed of a MarH ATP-dependent reductase and a MarDK catalytic core, whose architecture parallels nitrogenase. MarS complexes with MarDK to downregulate MAR activity during cellular sulfate influx, based on chromatographic and activity analyses. MarDK possesses complex metallocofactors resembling, but not identical to, nitrogenase P- and iron-only M-clusters, designated as mar1 and mar2 clusters based on metal, spectroscopic and mutagenesis analyses. They exhibit electronic features similar to the iron-only nitrogenase under turnover and, remarkably, are matured by MarB or nitrogenase NifB, resulting in maturase-dependent activity profiles. Altogether, this suggests a broader scope of reactivity, mechanisms and regulation in microbial metabolism for the nitrogenase-like family of enzymes than previously considered.

09 BIOMASS FUELS↗
DOE OSTI2026

Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms

Photobiocatalysis provides a powerful strategy for integrating light and biological catalysts to drive abiological transformations. However, its scalability is hindered by high enzyme loading, reliance on costly cofactors and instability under radical-generating conditions. Here we report the integration of light-driven enzymatic reactions into the cellular metabolism of Escherichia coli, bridging flavin-based photobiocatalysis with biosynthesis. Using synthetic biology strategies, we engineered microbial cells to continuously produce olefin substrates and ene-reductase while regenerating cofactors directly from glucose. By externally supplying radical precursors or introducing synthetic pathways for their in situ production, we enabled fermentation-based microbial photobiosynthesis, achieving high titres and demonstrating feasibility for scale-up in a bioreactor. This approach extends photobiocatalysis from in vitro applications to in vivo semi- and complete biosynthesis, revealing its full potential for integrating light-driven reactions into cellular metabolism.

Biocatalysis↗
DOE OSTI2025

Recent advances in enzyme engineering for improved deconstruction of poly(ethylene terephthalate) (PET) plastics

In the last ~20 years, a multitude of natural enzymes have been discovered that can catalyze the breakdown of the common plastic poly(ethylene terephthalate) (PET). While enzymatic PET recycling is an attractive alternative end-of-life route for this waste plastic, the enzymes are not yet optimized for efficient and economical industrial use. Here, we discuss recent advances in engineering these PET-degrading enzymes, which include PET, bis(2-hydroxyethyl) terephthalate (BHET), and 2-hydroxyethyl terephthalic acid (MHET) hydrolases, toward industrially-relevant engineering goals. We place emphasis on trends from past efforts in rational and semi-rational design and emerging areas in directed evolution/high throughput screening and computational design for engineering these enzymes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗