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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Artificial intelligence tools for enzyme engineering and metabolic engineering

Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.

Volk, Michael [Univ. of Illinois at Urbana-Champai↗
DOE OSTI2025

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

The discovery and engineering of new enzymes is important across the bioeconomy, with diverse applications from foods to pharmaceuticals, sensors to agriculture. However, enzyme engineering, in particular machine learning-guided engineering, is hampered by a lack of data. Currently there exists no database designed to capture and interpret datasets created in this domain, nor are there easy analysis and visualisation tools. We developed the Enzyme Engineering Database to provide a centralized resource and an online analysis tool to consolidate sequence-function data from enzyme engineering campaigns, thereby making three contributions: (i) a database into which researchers can deposit public data, (ii) visualisation and analysis tools for protein engineers to analyse their own data or compare enzyme variants to other engineering campaigns, and (iii) a gold-standard dataset for benchmarking automated extraction along with the first large language model extraction pipeline specific for enzyme engineering campaigns. The Enzyme Engineering Database is accessible at http://enzengdb.org/.

Long, Yueming [California Institute of Technology ↗
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 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 OSTI2026

TCF Base Technology-Specific Final Report: Engineering Enzymes for Crystalline PET Substrate

The primary objective of this project was to develop a new polyethylene terephthalate (PET) hydrolase enzyme to depolymerize relevant PET substrates for Birch Biosciences, using high-throughput protein expression, purification, and assaying systems and machine learning-guided enzyme design. As a secondary project objective, we also aimed to develop a more energy-efficient ethylene glycol (EG) recovery strategy relative to distillation.

09 BIOMASS FUELS↗
DOE OSTI2025

Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications

Covering: 2020 to 2025Natural products remain indispensable sources of therapeutic and bioactive compounds, yet traditional discovery strategies are constrained by compound rediscovery. Modular biosynthetic enzymes, such as type I polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs), offer promising platforms for combinatorial biosynthesis owing to their programmable architectures. However, practical implementation is frequently limited by inter-modular incompatibility and domain-specific interactions. This review highlights recent advances in modular enzyme assembly enabled by synthetic interfaces-including cognate docking domains, synthetic coiled-coils, SpyTag/SpyCatcher, and split inteins-which function as orthogonal, standardized connectors to facilitate post-translational complex formation. These interfaces support rational investigations into substrate specificity, module compatibility, and pathway derivatization as well as general enzyme clustering applications beyond PKS and NRPS systems. Synthetic interfaces can be integrated with computational tools to support a more systematic and scalable framework for modular enzyme engineering by providing predictive insights into domain compatibility and interface design. These approaches within iterative design-build-test-learn workflows can accelerate the programmable assembly of biosynthetic systems and expand the accessible chemical space for natural products.

Kim, Gahyeon↗
DOE OSTI2024

Final Technical Report

The Department of Energy is interested in technologies that support the sustainable production of fuels, chemicals, and other bioproducts from plant biomass, to offset the nation’s reliance on fossil resources. The plant cell wall of energy crops provides the largest reservoir of raw materials for bioproducts. However, the widespread use of plant cell walls is hampered by their complexity and resistance to breakdown. To improve the productivity and cost-effectiveness of using energy crops to generate bioproducts, the fundamental problem of deconstructing plant cell walls must be addressed. This project developed and evaluated an innovative genetic modification technology to produce strategically designed enzymes that specifically accumulate in the plant cell wall. The resulting enzyme-engineered energy crops are expected to grow normally under natural conditions but break down more quickly and easily under high temperature during the production of biobased products. As such, this plant cell wall targeting enzyme engineering effort will reduce the cost of plant cell wall deconstruction and ultimately improve the economics of bioproducts. The overall objective of this project is to develop and evaluate the in-planta enzyme engineering technology to reduce lignocellulose deconstruction cost. The concept was first validated using tobacco plant, a model plant system that is typically used in lab testing for initial concept validation. Then the enzyme optimization was validated using switchgrass, the energy crop to be used to produce bioproducts. There are three specific objectives in this Phase I project: (1) validate the enzyme optimization concept using tobacco plant, a model plant system. (2) validate the enzyme optimization concept using switchgrass. (3) techno-economic analysis (TEA) for further scale-up application. By the end of this project, in-planta enzyme engineering was validated in both tobacco and switchgrass plants, with improved enzyme activity and saccharification efficiency. The in-planta enzyme engineering in Tabacco didn’t have a significant impact on plant growth and development. Transgenic tobacco plants with in-planta cellulose degrading enzymes showed higher biomass digestibility than wild type. Gene construction and transformation in switchgrass was much longer than expected, which delayed the research progress. Besides, in-planta engineering of lignin degrading enzyme is more challenging than cellulose degrading enzyme, in terms of expression detection. Expression of lignin degrading enzyme and cellulose degrading enzyme improved biomass yield and saccharification efficiency of switchgrass, respectively. It is promising to express both genes in switchgrass for optimized overall performance. According to the results of TEA, switchgrass biomass production cost is mainly attributed to by fertility and harvesting. Biomass production profit can increase up to 10-fold depending on biomass price. The PHA production profit is also sensitive to the biomass price. The proposed technology could potentially reduce the biomass deconstruction cost from 33% to 9% of PHA revenue, making the biomass-based PHA competitive to petroleum-based polymers even in case of relatively high biomass price of biomass. Therefore, cultivation of the genetically engineered self-deconstruction switchgrass for Polyhydroxyalkanoate (PHA) production could benefit switchgrass grower and PHA producer with attractive profits for both sectors. This new enzyme optimization approach will be beneficial for bioindustries that use energy crops as feedstocks. It will improve the economic viability of converting energy crops to renewable products that support a sustainable society and helps address the Nation’s long-term strategic needs for renewable products and reduction of reliance on fossil resources.

42 ENGINEERING↗
DOE OSTI2026

Discovery and engineering of enzymes for new-to-nature photobiocatalysis

Photobiocatalysis integrates enzymatic catalysis with photochemistry, enabling challenging radical transformations with high selectivity under mild conditions. Early developments in this field were largely driven by the discovery that enzyme-bound cofactors can form photoactive charge–transfer complexes with substrates, thereby initiating radical chemistry upon light irradiation. Recent advances, however, have substantially expanded the mechanistic landscape of photobiocatalysis through diverse mechanisms. This review summarizes major developments in photobiocatalysis reported since 2024. Rather than cataloging individual reactions, we focus on the fundamental mechanisms of radical generation and interception within enzyme active sites, and discuss how these mechanistic principles guide the discovery, engineering, and design of enzymes for new-to-nature photobiocatalysis.

Bai, Zibo [University of Illinois Urbana-Champaign↗
DOE OSTI2026

Enzymatic Nylon Deconstruction: Enzyme Discovery, Engineering, and Opportunities

Nylons are widely used synthetic polyamides valued for their strength, versatility, and durability across diverse applications. However, their petrochemical origin and energy-intensive production underscore the need for efficient, circular solutions. Conventional recycling methods remain limited by incomplete recovery, material degradation, and costly sorting requirements. Enzymatic depolymerization offers a selective, low-energy alternative capable of processing mixed waste streams under mild conditions. While significant progress has been achieved for polyesters, enzymatic degradation of polyamides is still at an early stage. The discovery of nylon hydrolases demonstrated the potential of biological systems to evolve catalysts for synthetic polyamides, yet reported depolymerization yields remain low. These limitations reflect both the structural complexity of nylons and the need for improved enzyme discovery and engineering. In conclusion, this review highlights recent advances, key challenges, and future directions for enzymatic nylon recycling, outlining its potential role enabling mixed polymer waste to be used as a green feedstock for remanufacturing.

Amides↗
DOE OSTI2025

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

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↗
DOE OSTI2025

A framework for challenges and solutions in biodesign research

The bioeconomy represents an advanced economic paradigm that builds upon previous agricultural, industrial, and digital economic models. It seeks to tackle critical global challenges such as resource scarcity, escalating healthcare demands, and environmental degradation. At the heart of the bioeconomy is biomanufacturing, which uses natural or engineered enzymes or cell factories built from ​biological components like promoters, terminators, regulatory sequences, reporters, and functional genes into various chassis hosts (including animal, microbial, plant, and de novo systems) to create products such as food, energy, medicine, materials, chemicals, and engineered tissue/organs. An enabler of biomanufacturing is biodesign – also known as biosystems design and closely related to synthetic biology or engineering biology. This interdisciplinary field aims to understand and predictably modify existing life forms or create entirely new biological entities/systems using rational engineering strategies and automated design tools. Through these capabilities, biodesign supports the discovery, optimization, and creation of efficient platforms for biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stereospecific Enzymatic Conversion of Boronic Acids to Amines

Boronic acids and esters are highly regarded for their safety, unique reactivity, and versatility in synthesizing a wide range of small molecules, bioconjugates, and materials. They are not exploited in biocatalytic synthesis, however, because enzymes that can make, break, or modify carbon–boron bonds are rare. We wish to combine the advantages of boronic acids and esters for molecular assembly with biocatalysis, which offers the potential for unsurpassed selectivity and efficiency. Here, we introduce an engineered protoglobin nitrene transferase that catalyzes the new-to-nature amination of boronic acids using hydroxylamine. Initially targeting aryl boronic acids, we show that the engineered enzyme can produce a wide array of anilines with high yields and total turnover numbers (up to 99% yield and >4000 TTN), with water and boric acid as the only byproducts. We also demonstrate that the enzyme is effective with bench-stable boronic esters, which hydrolyze in situ to their corresponding boronic acids. Exploring the enzyme’s capacity for enantioselective catalysis, we found that a racemic alkyl boronic ester affords an enantioenriched alkyl amine, a transformation not achieved with chemocatalysts. The formation of an exclusively unrearranged product during the amination of a boronic ester radical clock and the reaction’s stereospecificity support a two-electron process akin to a 1,2-metallate shift mechanism. Here, the developed transformation enables new biocatalytic routes for synthesizing chiral amines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Biocatalyst discovery and design for plastics deconstruction: A multi‐scale perspective

Plastic waste accumulation poses significant environmental challenges due to a lack of economical solutions for the molecular deconstruction of diverse synthetic polymers. Biological‐based degradation offers promise but is hindered by the crystallinity, hydrophobicity, and additive complexity of plastics, which restrict biocatalyst access and activity. To address these problems, we propose a multi‐scale framework that combines detailed materials characterization, optimization of plastic‐biomolecular interfacial interactions, and enhancement of biocatalytic kinetics to develop effective plastic‐deconstructing enzymes. This approach leverages principles from reaction kinetics, transport and interfacial phenomena, and enzyme engineering to systematically address barriers across diverse plastic types. Our framework aims to accelerate the discovery and optimization of biocatalysts capable of scalable, selective, and efficient deconstruction of plastic waste. These advances hold potential to enable sustainable biological recycling and upcycling pathways, contributing to global efforts in mitigating plastic pollution and promoting circular material economies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Reaction Optimization for Enzymatic Deconstruction of Industrially Relevant Nylon Composites

Plastics such as polyamides (PAs) possess unique physicochemical properties that make them indispensable in modern society. However, their energy‐intensive production and challenging end‐of‐life management highlight the urgent need for efficient recycling or remanufacturing solutions. Enzymatic depolymerization offers a promising route toward circular recycling, yet remains constrained by limited enzyme characterization, lack of validation under industrially relevant conditions and substrates, and overall performance. Here, we optimized the reaction conditions for three recently discovered nylon‐degrading enzymes. One of them, Nyl12, achieved product titers with PA6 and PA66 that exceed previously reported values, without enzyme engineering or substrate pretreatment. We further demonstrated the scalability of the process and its application to complex PA‐based materials used in microelectronic components. Analysis of substrate features, including surface area and particle size, revealed key parameters governing enzymatic activity and provided a framework for future pretreatment and process optimization efforts. In combination, these efforts provide a new benchmark for enzymatic nylon recycling.

nylon↗
DOE OSTI2026

Molecular basis and biological relevance of bacterial and plant pinoresinol/lariciresinol reductase specificities

A bacterial pinoresinol/lariciresinol reductase (PLR) homolog named NrPinZ was obtained from a Novosphingobium rhizosphaerae sp. LY bacterial strain, with NrPinZ being part of its 5-step biochemical system catabolizing pinoresinol into coniferyl aldehyde and vanillin. Recombinant NrPinZ reduces racemic 8–8′ furanofuran lignans [(±)-pinoresinols, medioresinols, and syringaresinols] with similar overall catalytic efficiencies. In those reductions, only one of the two furan ring systems is reduced. Two other bacterial PLR homologs, NaPinZ and SlPinZ, from N. aromaticivorans F199 and Sphingobium lignivorans SYK-6, respectively, had comparable substrate versatilities and catalytic efficacies. Plant PLR homologs, by comparison, are either enantiospecific, enantioselective, or variants thereof, being able to reduce either one or both furan rings. For example, a recombinant enantioselective PLR (PLR_Tp2) from western red cedar (Thuja plicata) preferentially reduces both (+)-pinoresinol furan rings to afford (−)-secoisolariciresinol. BoltZ-2 modeling of NrPinZ and PLR_Tp2, together with substrate docking of (+)- and (−)-pinoresinols, medioresinols, and syringaresinols, was very instructive. The NrPinZ active site P1/P2 sub-pockets allow for both racemic forms to be catabolized. Conversely, the smaller P1 pocket in PLR_Tp2 preferentially positions (+)-pinoresinol for downstream metabolism into (−)-secoisolariciresinol, thereby providing a biochemical explanation for the different stereochemical outcomes. NrPinZ, NaPinZ, and SlPinZ, catalyzing substrate versatile catabolism of both racemic forms, may have important ramifications for gymnosperm and angiosperm lignin and lignan biodegradation, including its evolutionary significance and potential in enzyme engineering.

Boltz-2 molecular modeling↗
DOE OSTI2024

New Opportunities for Neutrons in Environmental and Biological Sciences

The use of neutron methods in environmental and biological sciences is rapidly emerging and accelerating with the development of new instruments at neutron user facilities. This article, based on a workshop held at Oak Ridge National Laboratory (ORNL), offers insights into the application of neutron techniques in environmental and biological sciences. Here we highlight recent advances and identify key challenges and potential future research areas. These include soil and rhizosphere processes, root water dynamics, plant-microbe interactions, structure and dynamics of biological systems, applications in synthetic biology and enzyme engineering, next-generation bioproducts, biomaterials and bioenergy, nanoscale structure, and fluid dynamics of porous materials in geochemistry. We provide an outlook on emerging opportunities with an emphasis on new capabilities that will be enabled at the Spallation Neutron Source Second Target Station currently under design at ORNL. The mission of scientific neutron user facilities worldwide is to enable science using state-of-the-art neutron capabilities. We aim to encourage researchers in the environmental and biological research community to explore the unique capability afforded by neutrons at these facilities.

54 ENVIRONMENTAL SCIENCES↗