Biocatalysis@TUDelft

Nature, Published online: 29 April 2026; doi:10.1038/s41586-026-10328-7

A Review of de novo protein design highlights key methodological advances and achievements, current challenges and future applications.

Nature Communications, Published online: 30 April 2026; doi:10.1038/s41467-026-72466-w

Penicillin derivatives remain among the most widely prescribed antibiotics. In this study, the authors report an alternative pathway to penicillins that uses standalone ligase and epimerase enzymes to generate peptide precursors, which can be transformed into penicillin derivatives using an engineered isopenicillin N synthase enzyme, providing direct access to therapeutically relevant penicillin G, penicillin V and ampicillin, which are currently produced by semisynthesis.

L-DOPA is a key therapeutic agent for Parkinsons disease, with growing demand due to global population aging. Here we report that heme-dependent tyrosine hydroxylase (TyrH) can utilize an ascorbate/O2 system--as an alternative to H2O2--to synthesize L-DOPA with markedly enhanced operational stability. While exogenous H2O2 rapidly inactivates TyrH within minutes, sodium ascorbate (NaAsc) enables sustained catalysis for up to 24 h, surpassing the H2O2-driven yield after only 30 min. UV-vis spectroscopy confirms that H2O2 readily degrades the heme center, whereas the heme remains intact in the presence of NaAsc. QM/MM simulations reveal that in situ generated H2O2 leads to the active species of Compound I for tyrosine hydroxylation. Through systematic optimization, we establish efficient reaction conditions (40 {micro}M TyrH, 1 mM L-Tyr, 100 mM NaAsc, pH 8.5, 40 {degrees}C), achieving >95% conversion of L-Tyr to L-DOPA within 2 h. This work not only provides a robust and sustainable biocatalytic route for L-DOPA production but also highlights the broader applicability of the ascorbate/O2 pathway in heme-enzyme catalysis.

Nature Communications, Published online: 25 April 2026; doi:10.1038/s41467-026-72354-3

Waste plastics pose an escalating environmental challenge, and existing disposal solutions remain inadequate. Industrial composting is labor and energy intensive, while engineered enzyme systems have yet to be deployable outside controlled facilities. In this study, the authors introduce an enzyme@MOF platform that can be incorporated into biodegradable plastics using industry-compatible processes. This strategy enables controlled, rain-triggered degradation under weakly acidic conditions, eliminating the need for collection or specialized composting. Notably, the resulting degradation products are biocompatible and even promote plant growth, highlighting the platform’s potential for sustainable, field-scale plastic remediation

Nature Synthesis, Published online: 28 April 2026; doi:10.1038/s44160-026-01065-w

Sandy Schmidt, a professor at the University of Groningen, talks to Nature Synthesis about the benefits and challenges to overcome in photoenzymatic synthesis.

Nature Catalysis, Published online: 28 April 2026; doi:10.1038/s41929-026-01528-5

Stereocontrol over radical intermediates is highly sought after in asymmetric organic synthesis, yet current approaches remain limited and difficult to generalize. A photobiocatalytic strategy employing thiamine diphosphate (ThDP)‑dependent enzymes now achieves simultaneous and precise control over two prochiral radical intermediates, enabling new‑to‑nature C(sp3)–C(sp3) bond formation with high enantio‑ and diastereoselectivity.

UDP-GlcA, the activated form of glucuronic acid, is essential for glycosylation and polysaccharide biosynthesis. Despite advances in UDP-GlcA synthesis, economical and scalable production methods remain limited. Here, we developed a multienzyme immobilization system for the continuous-flow synthesis of UDP-GlcA. We first constructed a UDP-glucose synthesis module that maintained stable operation for over 200 h with a space-time yield of 3.9 g·L⁻¹·h⁻¹. To address the bottleneck of the rate-limiting enzyme UDP-glucose dehydrogenase (TuaD), we obtained the mutant TuaD M8, using a combined strategy of protein repair one-stop shop engineering and rational reversion of synergistic deleterious mutations, achieving significantly enhanced activity and stability. Integration of both modules yielded a UDP-GlcA flow synthesis system with a space-time yield of 1.3 g·L⁻¹·h⁻¹ and 220 h continuous operation, demonstrating strong industrial potential. This strategy provides an efficient, sustainable, and cost-effective approach for large-scale UDP-GlcA production and establishes a framework for biosynthesizing other high-value nucleotide sugars via immobilized enzyme systems.

PM0042, a heme-degrading enzyme from Pasteurella multocida, contains a unique C-terminal glycine–histidine (GH) repeat motif. Fe²⁺ binding to this motif enhances catalytic activity threefold. This enhancement occurs without significant structural changes to the heme environment; instead, the GH-bound Fe²⁺ functions as an electron mediator between the reductant and the heme iron.

ABSTRACT

PM0042 from Pasteurella multocida is a heme-degrading enzyme homologous to HutZ from Vibrio cholerae, but uniquely contains a glycine–histidine (GH) repeat motif at its C-terminal region. Unlike HutZ, PM0042 exhibits a threefold increase in heme degradation activity upon Fe²⁺ addition, yet the underlying mechanism has remained unclear. Here, we investigated the effect of Fe²⁺ on the catalytic process of PM0042. Spectroscopic analyses revealed that Fe^{2 +} binding does not induce structural changes at either distal or proximal heme sites. Kinetic studies of individual steps in the degradation pathway demonstrated that the reduction of ferric heme to ferrous heme is the rate-determining step and is markedly accelerated by Fe²⁺. Other steps, including O₂ binding, verdoheme formation, and biliverdin production, were unaffected. Mutational analysis introducing a His-rich motif into HutZ confirmed that Fe²⁺ enhances activity when bound near the proximal site. These findings suggest that Fe²⁺ acts as an electron mediator rather than a structural modulator, facilitating electron transfer from reductant to heme iron. This study provides mechanistic insight into metal-assisted catalysis in bacterial heme degradation and highlights the functional role of GH repeat sequences in electron transfer.

Here, we show that well studied PET hydrolases can be re-engineered via directed evolution to deconstruct alternative aromatic-containing commodity polymers. Introduction of only three mutations into LCC^ICCG was sufficient to generate an efficient polycarbonate hydrolase with high operational stability that can fully depolymerize a polycarbonate sample within 6 h at 75°C.

ABSTRACT

We recently developed a high-throughput directed evolution platform for engineering polymer degrading enzymes, and showcased its utility through the development of an efficient and thermostable variant of IsPETase, termed HotPETase. Here, we show that this platform can be used to re-engineer PET degrading enzymes for the recycling of other aromatic-containing commodity polymers. Promiscuous poly(bisphenol-A carbonate) (PC) depolymerase activity of LCC^ICCG was enhanced by directed evolution to afford an engineered polycarbonate hydrolase, that also benefits from improved solvent tolerance and operational stability at elevated temperatures. Interestingly, the enzyme-concentration dependent inhibition observed with the parent enzyme is also alleviated through evolution, improving practical utility. PC-2 can achieve rapid and complete depolymerization of a PC film to bisphenol-A (BPA) in just 6 h at 75°C. This study shows how plastic degrading enzymes can be readily adapted through evolution to operate on new and valuable polymer classes.

Association of the L-cluster with the nitrogenase assembly proteins NifEN (NifEN^L) or NifB (NifB^L) intrinsically endows these proteins with N₂-reducing activity, enabling in vitro N₂-reduction by NifEN^L and NifB^L when supplied with chemical reductants or photoexcited quantum dots while supporting in vivo N₂-fixation in NifEN^L- and NifEN^L-expressing Escherichia coli strains where the low-potential ferredoxin YfhL serves as the electron donor.

ABSTRACT

The Mo-nitrogenase, which consists of a reductase component (NifH) and a catalytic component (NifDK), catalyzes ATP-dependent reduction of N₂ to NH₃ at its active-site M-cluster ([(R-homocitrate)MoFe₇S₉C]). A complex metallocofactor, the M-cluster is assembled through NifB-mediated formation of the intermediate L-cluster ([Fe₈S₉C]), followed by L-to-M cluster maturation on NifEN. Here, we show that the L-cluster intrinsically endows the assembly proteins NifB and NifEN with N₂-reducing activity. Such a function is strictly dependent on the L-cluster, as NifB acquires N₂-reducing capability only after conversion of the precursor K-cluster (2x[Fe₄S₄]) to an L-cluster. Both L-cluster-bound NifB (NifB^L) and NifEN (NifEN^L) catalyze ATP-independent N₂ reduction in vitro when supplied with a chemical reductant or photoexcited quantum dots. Moreover, these L-cluster-containing proteins support in vivo N₂-fixation in NifH-deficient E. coli strains, where the low-potential ferredoxin YfhL serves as an essential physiological electron donor. The intrinsic reactivity of the L-cluster toward N₂ supports an evolutionary model in which primordial nitrogenase was a simpler, one-component, NifEN^L-like enzyme that preceded the modern, high-efficiency two-component system; whereas the shared L-cluster topology found in ancient nondiazotrophic enzymes like methyl-CoM reductase and methylthio-alkane reductase further implies that the L-cluster may represent an evolutionary link among nitrogen, carbon, and sulfur biogeochemical cycles.

Nature, Published online: 27 April 2026; doi:10.1038/d41586-026-01283-4

Low-cost system can optimize synthesis of a wide variety of products.

NH2 -MIL-101(Fe) is a promising support for CA immobilization, enabling efficient and reusable biocatalytic CO₂ capture systems with potential for scalable environmental applications

ABSTRACT

The increasing concentration of atmospheric carbon dioxide (CO₂), primarily from fossil fuel combustion, poses a significant environmental threat and necessitates effective capture technologies. Carbonic anhydrase (CA), a zinc-containing metalloenzyme, has garnered attention for its exceptional catalytic efficiency in accelerating CO₂ hydration. However, its industrial application is limited by thermal instability, short operational lifespan, and poor reusability. This study investigates the immobilization of CA onto the biocompatible metal-organic framework, NH₂-MIL-101(Fe) to enhance enzyme stability and reusability for CO₂ capture applications. The MOF was synthesized and characterized by XRD, FTIR, BET, SEM, TEM, TGA, and EDX. Enzyme loading and immobilization efficiency were quantified, yielding a loading of 0.0394 mg CA/mg MOF and an immobilization efficiency of 60%. Activity assays demonstrated an 80% retention of catalytic function post-immobilization. Thermal stability tests showed significantly improved enzyme resilience at elevated temperatures, and the composite retained 40% of its activity after six reuse cycles. In CO₂ capture experiments, the CA/MOF composite achieved a CaCO₃ yield comparable to that of free CA, with the added benefit of enhanced operational stability. This study confirms that NH₂-MIL-101(Fe) is a promising support for CA immobilization, enabling efficient and reusable biocatalytic CO₂ capture systems with potential for scalable environmental applications.