Enhancement of bioelectrochemical dioxygen reduction with oxygen-enriching materials

Bioelectrochemical dioxygen reduction reaction (ORR) catalyzed by multi-copper oxidases (MCOs) is a process of paramount importance occurring at the cathode of enzymatic biofuel cells (EBFCs), which is an energy harvester that holds promise of self-sustained implantable and wearable medical devices. The MCO biocathode is, however, frequently the limiting factor of a working EBFC. Besides the operational stability issue, enzymatic biocathodes are largely constrained by the relatively low solubility of dioxygen in aqueous solution. As an emerging topic, we here review the introduction of dioxygen-enriching materials to the cathodic bioelectrode for overcoming the dioxygen supply limitation, leading to improved ORR performance.     

Immobilizing redox enzymes at mesoporous and nanostructured electrodes

Three key challenges are stimulating intensive research in the development of productive direct electron transfer mode enzyme electrodes: proper enzyme orientation, high enzyme loading, and full retention of enzyme activity. In this review, we summarize some significant advances that have been reported in the last years on the design of mesoporous and nanostructured electrodes as enzyme scaffolds and of innovative methodologies for wiring enzymes to electrodes. Particular attention is given to investigations on physical factors that determine a favorable enzyme immobilization, to provide rational guidelines for the design of productive enzymatic electrodes. Finally, some emerging trends focused on the spatial organization of either single enzymes or enzyme cascades are also briefly addressed.     

Sonication enhances the stability of MnO2 nanoparticles on silk film template for enzyme mimic application

We have developed an in-situ method using sonication (3 mm probe sonicator, 30 W, 20 kHz) and auto-reduction (control) to study the mechanism of the formation of manganese dioxide (MnO₂) on a solid template (silk film), and its resulting enzymatic activity on tetramethylbenzidine (TMB) substrate. The fabrication of the silk film was first optimized for stability (no degradation) and optical transparency. A factorial approach was used to assess the effect of sonication time and the initial concentration of potassium permanganate (KMnO₄). The result indicated a significant correlation with a fraction of KMnO₄ consumed and MnO₂ formation. Further, we found that the optimal process conditions to obtain a stable silk film with highly catalytic MnO₂ nanoparticles (NPs) was 30 min of sonication in the presence of 0.5 mM of KMnO₄ at a temperature of 20–24 °C. Under the optimal condition, we monitored in-situ the formation of MnO₂ on the silk film, and after thorough rinsing, the in-situ catalysis of 0.8 mM of TMB substrate. For control, we used the auto-reduction of KMnO₄ onto the silk film after about 16 h. The result from single-wavelength analysis confirmed the different kinetics rates for the formation of MnO₂ via sonication and auto-reduction. The result from the multivariate component analysis indicated a three components route for sonication and auto-reduction to form MnO₂-Silk. Overall, we found that the smaller size, more mono-dispersed, and deeper buried MnO₂ NPs in silk film prepared by sonication, conferred a higher catalytic activity and stability to the hybrid material.     

ABLE: Attention based learning for enzyme classification

Classifying proteins into their respective enzyme class is an interesting question for researchers for a variety of reasons. The open source Protein Data Bank (PDB) contains more than 1,60,000 structures, with more being added everyday. This paper proposes an attention-based bidirectional-LSTM model (ABLE) trained on over sampled data generated by SMOTE to analyse and classify a protein into one of the six enzyme classes or a negative class using only the primary structure of the protein described as a string by the FASTA sequence as an input. We achieve the highest F1-score of 0.834 using our proposed model on a dataset of proteins from the PDB. We baseline our model against eighteen other machine learning and deep learning networks, including CNN, LSTM, Bi-LSTM, GRU, and the state-of-the-art DeepEC model. We conduct experiments with two different oversampling techniques, SMOTE and ADASYN. To corroborate the obtained results, we perform extensive experimentation and statistical testing.     

Enzyme-catalyzed asymmetric domino aza-Michael/aldol reaction for the synthesis of 1,2-dihydroquinolines using pepsin from porcine gastric mucosa

An unprecedented enzyme-catalyzed asymmetric domino aza-Michael/aldol reaction of 2-aminobenzaldehyde and a,b-unsaturated aldehydes is achieved. Pepsin from porcine gastric mucosa provided mild and efficient access to diverse substituted 1,2-dihydroquinolines in yields of 38%–97% with 6%–24%enantiomeric excess(ee). This work not only provides a novel method for the synthesis of dihydroquinoline derivatives, but also promotes the development of enzyme catalytic promiscuity.     

Asymmetric synthesis of 1,3-oxathiolan-5-one derivatives through dynamic covalent kinetic resolution

The asymmetric synthesis of 1,3-oxathiolan-5-one derivatives through an enzyme-catalyzed, dynamic covalent kinetic resolution strategy is presented. Dynamic hemithioacetal formation combined with intramolecular, lipase-catalyzed lactonization resulted in good conversions with moderate to good enantiomeric excess (ee) for the final products. The process was evaluated for different lipase preparations, solvents, bases, and reaction temperatures, where lipase B from Candida antarctica (CAL-B) proved most efficient. The substrate scope was furthermore explored for a range of aldehyde structures, together with the potential access to nucleoside analog inhibitor core structures.     

MALDI Imaging Assisted Discovery of a Di-O-glycosyltransferase from Platycodon grandiflorum Root

A matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) assisted genome mining strategy was developed for the discovery of glycosyltransferase (GT) from the root of Platycodon grandiflorum. A di-O-glycosyltransferase PgGT1 was discovered and characterized that is capable of catalyzing platycoside E (PE) synthesis through the attachment of two β-1,6-linked glucosyl residues sequentially to the glucosyl residue at the C3 position of platycodin D (PD). Although UDP-glucose is the preferred sugar donor for PgGT1, it could also utilize UDP-xylose and UDP-N-acetylglucosamine as weak donors. Residues S273, E274, and H350 played important roles in stabilizing the glucose donor and positioning the glucose in the optimal orientation for the glycosylation reaction. This study clarified two key steps involved in the biosynthetic pathway of PE and could greatly contribute to improving its industrial biotransformation.     

A New Thiolate-Bound Dimanganese Cluster as a Structural and Functional Model for Class Ib Ribonucleotide Reductases

In class Ib ribonucleotide reductases (RNRs) a dimanganese(II) cluster activates superoxide (O₂⋅⁻) rather than dioxygen (O₂), to access a high valent Mn^III−O₂−Mn^IV species, responsible for the oxidation of tyrosine to tyrosyl radical. In a biomimetic approach, we report the synthesis of a thiolate-bound dimanganese complex [Mn^II₂(BPMT)(OAc)₂](ClO)₄ (BPMT=(2,6-bis{[bis(2-pyridylmethyl)amino]methyl}-4-methylthiophenolate) ( 1 ) and its reaction with O₂⋅⁻ to form a [(BPMT)MnO₂Mn]²⁺ complex 2 . Resonance Raman investigation revealed the presence of an O−O bond in 2 , while EPR analysis displayed a 16-line S_t=1/2 signal at g=2 typically associated with a Mn^IIIMn^IV core, as detected in class Ib RNRs. Unlike all other previously reported Mn−O₂−Mn complexes, generated by O₂⋅⁻ activation at Mn₂ centers, 2 proved to be a capable electrophilic oxidant in aldehyde deformylation and phenol oxidation reactions, rendering it one of the best structural and functional models for class Ib RNRs.     

Didepside Formation by the Nonreducing Polyketide Synthase Preu6 of Preussia isomera Requires Interaction of Starter Acyl Transferase and Thioesterase Domains

Orsellinic acid (OA) derivatives are produced by filamentous fungi using nonreducing polyketide synthases (nrPKSs). The chain-releasing thioesterase (TE) domains of such nrPKSs were proposed to also catalyze dimerization to yield didepsides, such as lecanoric acid. Here, we use combinatorial domain exchanges, domain dissections and reconstitutions to reveal that the TE domain of the lecanoric acid synthase Preu6 of Preussia isomera must collaborate with the starter acyl transferase (SAT) domain from the same nrPKS. We show that artificial SAT-TE fusion proteins are highly effective catalysts and reprogram the ketide homologation chassis to form didepsides. We also demonstrate that dissected SAT and TE domains of Preu6 physically interact, and SAT and TE domains of OA-synthesizing nrPKSs may co-evolve. Our work highlights an unexpected domain–domain interaction in nrPKSs that must be considered for the combinatorial biosynthesis of unnatural didepsides, depsidones, and diphenyl ethers.