Pyrroloquinoline quinone (PQQ) is a bacterial redox cofactor enabling enzyme catalysis in various sugar and alcohol dehydrogenases. However, its proposed additional role as a "longevity vitamin" lacks a clear molecular basis and is thus highly debated. Here, we applied chemical proteomics to identify previously unknown classes of PQQ-binding proteins. We designed and synthesized a structurally diverse suite of five PQQ probes equipped with a diazirine photo-cross-linker and an alkyne handle for target identification. The fidelity of the probes was first evaluated for two well-characterized bacterial PQQ-dependent enzymes, demonstrating not only probe binding but also the reconstitution of catalytic activity. We then commenced with proteome profiling of Escherichia coli and Pseudomonas putida cells and unraveled a distinct set of putative PQQ-binding proteins. Recombinant expression of selected hits, including several chaperones, validated PQQ binding. Notably, in some cases, PQQ even formed covalent adducts with selected lysine residues, for instance, in the AAA+ ATPase RuvB involved in DNA remodeling. Overall, our work highlights the utility of PQQ probes to further unravel the complement of cofactor-binding proteins in whole cells. It also provides a basis for future mechanistic studies of PQQ functions beyond redox catalysis.

De novo designed metalloenzymes and photoenzymes are a valuable addition to the biocatalytic toolbox. We previously introduced PhotoLanZymes (PLZ), a family of lanthanide-dependent photoredox enzymes that enable radical carbon-carbon bond cleavages of diol substrates upon Ce(iii/iv) binding and visible-light irradiation. While rational optimization increased their catalytic activity and photostability, the first generation of PLZ variants was limited by slow lanthanide binding and a lack of enantioselectivity. Here, we demonstrate that coupling computational redesign with directed evolution provides an effective strategy to overcome these limitations. First, we reduced the cavity size to enhance substrate interactions with the protein's active site, which facilitated initial enantiocontrol. Simultaneously, the AI-guided redesign approach improved the lanthanide binding kinetics. We then performed directed evolution to selectively accelerate the photocatalytic turnover for one of the substrate enantiomers, yielding a PLZ variant with markedly improved enantioselectivity. These results underscore the value of integrating AI-guided protein design with laboratory evolution to obtain stereoselective de novo metalloenzymes and photoenzymes.

The design of artificial photoenzymes by incorporating synthetic chromophores into proteins represents a promising strategy to achieve non-natural biocatalytic transformations with high levels of stereocontrol. Selecting an appropriate protein scaffold is a crucial step in this approach, which so far has been limited to naturally occurring proteins. Here, we tested the suitability of computationally designed scaffolds for this purpose. We chose a de novo helical bundle protein that has a central cavity for small molecule binding but no inherent catalytic activity. To generate a starting point for photoenzyme engineering, we installed a thioxanthone-based triplet sensitizer via cysteine bioconjugation. Guided by computational modeling and molecular dynamics (MD) simulations, three rounds of directed evolution toward the [2 + 2] photocycloaddition of a 3-alkenyloxy-substituted quinolone resulted in enzyme variants with catalytic efficiencies of k(cat)/K-m > 1000 M-1 s(-1) and opposite enantioselectivity. Upon visible-light irradiation, both product enantiomers were accessible with quantitative yield and >90:10 enantiomeric ratio. Furthermore, we obtained high-resolution crystal structures of the evolved designer enzymes. When exposing crystals of substrate-bound protein to blue light, we observed product formation in crystallo and could rationalize the enantioselectivity. Our work highlights the potential of de novo designed protein scaffolds to efficiently generate and evolve stereoselective artificial photoenzymes.

Incorporating metal cofactors into computationally designed protein scaffolds provides a versatile route to novel protein functions, including the potential for new-to-nature enzyme catalysis. However, a major challenge in protein design is to understand how the scaffold architecture influences conformational dynamics. Here, we characterized structure and dynamics of a modular de novo scaffold with flexible inter-domain linkers. Three rationally engineered variants with different metal specificity were studied by combining X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations. The lanthanide-binding variant was initially trapped in an inactive conformational state, which impaired efficient metal coordination and cerium-dependent photocatalytic activity. Stabilization of the active conformation by AI-guided sequence optimization using ProteinMPNN led to accelerated lanthanide binding and a 10-fold increase in kcat/Km for a photoenzymatic model reaction. Our results suggest that modular scaffold architectures provide an attractive starting point for de novo metalloenzyme engineering and that ProteinMPNN-based sequence redesign can stabilize desired conformational states.

Photoenzymatic catalysis facilitates stereoselective new-to-nature chemistry under mild conditions. In addition to the rational design of artificial photoenzymes, naturally occurring redox enzymes have been repurposed for this approach. Most prominently, flavin-containing cofactors can promote photoredox catalysis in the chiral protein environment, with several examples of enantioselective C–C bond forming reactions reported in recent years. Here, we add another class of natural enzymes, which utilize the pyrroloquinoline quinone (PQQ) cofactor, to the toolbox of photobiocatalysis. Although structurally distinct from flavin, PQQ exhibits mechanistic similarities, as it also absorbs visible light and is capable of single-electron transfer. First, we established the trimethyl ester PQQMe3 as a stand-alone photoredox catalyst in pure organic solvent. Upon excitation, PQQMe3 enables the redox-neutral radical cyclization of an N-(bromoalkyl)-substituted indole. We then tested a panel of PQQ-dependent sugar and alcohol dehydrogenases for photoenzymatic catalysis in aqueous buffer, focusing on a redox-neutral radical reaction to form oxindoles. Under optimized reaction conditions, we obtained 69% yield and an 82:18 enantiomeric ratio. Our work thus demonstrates that PQQ enzymes are capable of stereoselective photoredox catalysis. Future enzyme engineering efforts based on computational modelling and directed evolution will fully unlock their synthetic potential.

The specific incorporation of lanthanide ions is a promising strategy to equip biomolecules with a new function. Their long-lived luminescence, strong anomalous X-ray scattering, paramagnetism, Lewis acidity, and photoredox activity are attractive features for protein-based probes, materials, and catalysts. However, natural lanthanide-binding proteins are rare, and de novo design is often complicated by unspecific binding to negatively charged patches on protein surfaces. We thus aimed to develop an efficient workflow to screen libraries of protein scaffolds for their ability to coordinate lanthanides. Here, we introduce a microtiter plate-based assay, which employs commercial filter plates and a dual readout based on sensitized Tb3+ luminescence. We first benchmarked our procedure using control proteins with and without lanthanide-binding sites, demonstrating that site-specific coordination and surface binding can be distinguished. The stringency of this protocol also allowed screening for small lanthanide-binding peptides in the presence of a large expression tag. We then designed a de novo scaffold library derived from a helical bundle protein and applied our screening platform. We could identify lanthanide-binding variants with nanomolar affinity, distinct lanthanide specificity, and increased thermostability in response to metal binding. Our approach will support the discovery and evolution of lanthanide-binding peptides and proteins for various applications in vitro and in living cells.

Photoenzymatic catalysis facilitates stereoselective new-to-nature chemistry under mild conditions. In addition to the rational design of artificial photoenzymes, naturally occurring redox enzymes can be repurposed to promote photoredox catalysis in the chiral protein environment. Here, we show that enzymes utilizing the pyrroloquinoline quinone (PQQ) cofactor expand the toolbox of photobiocatalysis. PQQ absorbs visible light and is capable of single-electron transfer. It thus exhibits mechanistic similarities to flavin cofactors, which are widely used for photoenzymatic approaches. First, we established the trimethyl ester PQQMe3 as a stand-alone photoredox catalyst in pure organic solvent. Upon excitation, PQQMe3 enables the redox-neutral radical cyclization of an N-(bromoalkyl)-substituted indole. We then tested a panel of PQQ-dependent sugar and alcohol dehydrogenases for photoenzymatic catalysis in aqueous buffer, focusing on a redox-neutral radical reaction to form oxindoles. Under optimized reaction conditions, we obtained a 69% yield and an 82:18 enantiomeric ratio. Our work thus demonstrates that PQQ enzymes are capable of stereoselective photoredox catalysis. Future enzyme engineering efforts based on computational modeling and directed evolution will fully unlock their synthetic potential.

Due to their distinct magnetic and optical properties, lanthanides are an essential resource for many modern technologies. The increasing knowledge on lanthanide-utilizing bacteria, and the proteins they evolved to specifically bind these metals, fosters new strategies towards bio-inspired lanthanide recycling and separation. Furthermore, de novo designed proteins have been equipped with lanthanide binding sites to develop functional tools such as MRI contrast agents or artificial photoenzymes.

Photocatalysis is a versatile and rapidly developing field with applications spanning artificial photosynthesis, photo-biocatalysis, photoredox catalysis in solution or supramolecular structures, utilization of abundant metals and organocatalysts, sustainable synthesis, and plastic degradation. In this Perspective, we summarize conclusions from an interdisciplinary workshop of young principal investigators held at the Lorentz Center in Leiden in March 2023. We explore how diverse fields within photocatalysis can benefit from one another. We delve into the intricate interplay between these subdisciplines, by highlighting the unique challenges and opportunities presented by each field and how a multidisciplinary approach can drive innovation and lead to sustainable solutions for the future. Advanced collaboration and knowledge exchange across these domains can further enhance the potential of photocatalysis. Artificial photosynthesis has become a promising technology for solar fuel generation, for instance, via water splitting or CO2 reduction, while photocatalysis has revolutionized the way we think about assembling molecular building blocks. Merging such powerful disciplines may give rise to efficient and sustainable protocols across different technologies. While photocatalysis has matured and can be applied in industrial processes, a deeper understanding of complex mechanisms is of great importance to improve reaction quantum yields and to sustain continuous development. Photocatalysis is in the perfect position to play an important role in the synthesis, deconstruction, and reuse of molecules and materials impacting a sustainable future. To exploit the full potential of photocatalysis, a fundamental understanding of underlying processes within different subfields is necessary to close the cycle of use and reuse most efficiently. Following the initial interactions at the Lorentz Center Workshop in 2023, we aim to stimulate discussions and interdisciplinary approaches to tackle these challenges in diverse future teams.

The development of artificial metalloenzymes (ArMs) aims to expand the capabilities of enzymatic catalysis, most notably towards new reaction mechanisms. Frequently, ArMs harness metal cofactors that are not naturally found in enzymes and embed these in specifically selected or designed protein scaffolds. ArMs have been developed for a wide range of natural and non-natural reactions, underscoring their potential to revolutionize fields such as biocatalysis or metabolic engineering. At the same time, replicating the catalytic prowess of natural enzymes is a highly challenging task, and several limitations need to be overcome to make ArM catalysis widely applicable. In this Primer, we introduce the state of the art in designing and engineering ArMs, describing best practices and important examples and achievements. Moreover, we consider potential applications of ArMs, as well as outstanding challenges, and discuss how these may be addressed in the coming years. Artificial metalloenzymes harness metal cofactors that are not naturally found in enzymes and embed these in specifically selected or designed protein scaffolds. In this Primer, Vornholt et al. describe the best practices for designing and engineering artificial metalloenzymes.

Cerium photoredox catalysis has emerged as a powerful strategy to activate molecules under mild conditions. Radical intermediates are formed using visible light and simple complexes of the earth-abundant lanthanide. However, it remains a major challenge to achieve stereocontrol in these reactions. Here, we report an artificial photoenzyme enabling this chemistry inside a protein. We utilize a de novo designed protein scaffold that tightly binds lanthanide ions in its central cavity. Upon visible-light irradiation, the cerium-dependent enzyme catalyzes the radical C–C bond cleavage of 1,2-diols in aqueous solution. Protein engineering led to variants with improved photostability and initial stereoselectivity. The photoenzyme cleaves a range of aromatic and aliphatic substrates, including lignin surrogates. Surface display of the protein scaffold on E. coli facilitates whole-cell photobiocatalysis. Furthermore, we show that also natural lanthanide-binding proteins are suitable for this approach. Our study thus demonstrates a new-to-nature enzymatic photoredox activity with broad catalytic potential.

Promethium is the only Lanthanide (Ln) that exists exclusively as unstable isotopes, which consequently prevents its occurrence in appreciable amounts in nature. Lns have shown to be biologically relevant for methanotrophic and methylotrophic bacteria. This paper presents growth studies on the methanotrophic bacterium Methylacidiphilum fumariolicum SolV with Pm-147 along with enzymatic assays of its Ln-dependent methanol dehydrogenase. The results indicate that Pm is positioned precisely as assumed within the Ln series in a biological context, despite its radioactivity.

Exploring new fields: Lanthanide-using bacteria that turn over methane or methanol in their metabolism can replace essential lanthanides by certain actinides. In their Research Article (e202303669), Lena J. Daumann et al. show that an extremophile isolated from a volcanic mud-pot as well as a methylotrophic laboratory strain can use americium and curium. In vivo growth experiments as well as in vitro studies with the key metabolic enzyme methanol dehydrogenase support that these actinides can sustain the one-carbon metabolism of these bacteria.

AbstractCertain f‐block elements—the lanthanides—have biological relevance in the context of methylotrophic bacteria. The respective strains incorporate these 4 f elements into the active site of one of their key metabolic enzymes, a lanthanide‐dependent methanol dehydrogenase. In this study, we investigated whether actinides, the radioactive 5 f elements, can replace the essential 4 f elements in lanthanide‐dependent bacterial metabolism. Growth studies with Methylacidiphilum fumariolicum SolV and the Methylobacterium extorquens AM1 ΔmxaF mutant demonstrate that americium and curium support growth in the absence of lanthanides. Moreover, strain SolV favors these actinides over late lanthanides when presented with a mixture of equal amounts of lanthanides together with americium and curium. Our combined in vivo and in vitro results establish that methylotrophic bacteria can utilize actinides instead of lanthanides to sustain their one‐carbon metabolism if they possess the correct size and a +III oxidation state.

The biological relevance of early lanthanides, such as neodymium, remained undiscovered until methylotrophic bacteria with lanthanide-dependent metabolism were identified. The respective strains incorporate these elements into the active site of their key metabolic enzyme methanol dehydrogenase (MDH). Growth studies with the strictly lanthanide-dependent thermoacidophile Methylacidiphilum fumariolicum SolV and the mesophilic Methylorubrum extorquens AM1 ΔmxaF mutant demonstrate that the trivalent actinides americium and curium support growth in the absence of the essential lanthanides. In fact, the bacteria make no distinction between lanthanide and actinide ions if they have the correct size and oxidation state. Time-resolved laser-induced fluorescence spectroscopy, liquid scintillation counting, and inductively coupled plasma mass spectrometry confirm the bacterial uptake. The interchangeability of f-block elements is supported by very similar enzymatic activities of recombinant methanol dehydrogenase reconstituted with different metal ions. Our combined in vivo and in vitro results firmly establish that actinides support growth of methylotrophic bacteria, suggesting a potential biological role for these radioactive elements. Importantly, bacteria capable of utilizing actinides will also be able to mobilize these elements in the environment. This may lead to applications for bioremediation and recycling/separation of lanthanides and actinides.

AbstractÜber spezialisierte Enzyme, Affinitätsselektionsmethoden, um bioaktive Substanzen zu entdecken, hochauflösende Strukturanalyse von Proteinkomplexen und die Kombination von Bio‐ und Photokatalyse.