Thermal Atomization of Platinum Nanoparticles into Single Atoms: An Effective Strategy for Engineering High-Performance Nanozymes.

Although great progress has been made in artificial enzyme engineering, their catalytic performance is far from satisfactory as alternatives of natural enzymes. Here, we report a novel and efficient strategy to access high-performance nanozymes via direct atomization of platinum nanoparticles (Pt NPs) into single atoms by reversing the thermal sintering process. Atomization of Pt NPs into single atoms makes metal catalytic sites fully exposed and results in engineerable structural and electronic properties, thereby leading to dramatically enhanced enzymatic performance. As expected, the as-prepared thermally stable Pt single-atom nanozyme (PtTS-SAzyme) exhibited remarkable peroxidase-like catalytic activity and kinetics, far exceeding the Pt nanoparticle nanozyme. The following density functional theory calculations revealed that the engineered P and S atoms not only promote the atomization process from Pt NPs into PtTS-SAzyme but also endow single-atom Pt catalytic sites with a unique electronic structure owing to the electron donation of P atoms, as well as the electron acceptance of N and S atoms, which simultaneously contribute to the substantial enhancement of the enzyme-like catalytic performance of PtTS-SAzyme. This work demonstrates that thermal atomization of the metal nanoparticle-based nanozymes into single-atom nanozymes is an effective strategy for engineering high-performance nanozymes, which opens up a new way to rationally design and optimize artificial enzymes to mimic natural enzymes.

Production of new nanobiocatalysts via immobilization of lipase B from C. antarctica on polyurethane nanosupports for application on food and pharmaceutical industries.

Nanobiocatalysts were produced via immobilization of CalB lipase on polyurethane (PU) based nanoparticles and their application on the synthesis of important industrial products was evaluated. Nanoparticles of polyurethane functionalized with poly(ethylene glycol) (PU-PEG) were synthetized through miniemulsion polymerization and the addition of crosslinking agents were evaluated. The nanoparticles were employed as support for CalB and the kinetic parameters were reported. The performance of new biocatalysts was evaluated on the hydrolysis reaction of p-NPB and on the enantioselective hydrolysis of (R,S)-mandelic acid. The esterification reaction was evaluated on the production of ethyl esters of Omega-3. The effect of poly(ethylene glycol) molar mass (400, 4000 or 6000 Da)on the biocatalyst activity was also analyzed. The PU-PEG6000-CalB showed the highest value of the kinetic parameters, highlighting the high reaction rate. The addition of trehalose as crosslinking agent improved the thermal stability of the biocatalysts. PU-PEG400-CalB was the most active nanobiocatalyst, exhibiting a ethyl esters production of 43.72 and 16.83 mM.U -1 using EPA and DHA, respectively. The nanobiocatalyst was also applied in enantiomeric resolution of mandelic acid, showing promising enantiomeric ratios. The results obtained in this work present alternative and sustainable routes for the synthesis of important compounds used on food and pharmaceutical industries.

Clinical potential of a rationally engineered enzyme for treatment of cocaine dependence: Long-lasting blocking of the psychostimulant, discriminative stimulus, and reinforcing effects of cocaine.

It is a grand challenge to develop a truly effective treatment of substance use disorder (SUD), particularly for cocaine and other drugs without an FDA-approved treatment available, because a truly effective therapy must effectively block the drug's physiological and reinforcing effects during the entire period of treatment in order to achieve the long-time abstinence required by the FDA. Whether a biologic, such as monoclonal antibody, vaccine, or therapeutic enzyme, can be truly effective for SUD treatment or not has been the subject of extensive debate. The main debate question is whether a biologic, particularly an exogenous enzyme, can effectively block the drug's reinforcing effect. In this report, we demonstrate that a modest dose of a recently redesigned long-acting cocaine hydrolase, CocH3-Fc(M6), can be used to effectively block the psychostimulant, discriminative stimulus, and reinforcing effects of cocaine for a sufficiently long period of time. For example, a dose of 3 mg/kg CocH3-Fc(M6) completely blocked the discriminative stimulus and reinforcing effects for 24/25 days and continued to significantly attenuate/decrease the cocaine effects for at least 29 days in rats. All the animal data consistently suggest that the long-acting cocaine hydrolase is a truly promising candidate of enzyme therapy for treatment of cocaine use disorder.

Artificial Metalloenzymes: Recent Developments and Innovations in Bioinorganic Catalysis.

Cellular life is orchestrated by the biochemical components of cells that include nucleic acids, lipids, carbohydrates, proteins, and cofactors such as metabolites and metals, all of which coalesce and function synchronously within the cell. Metalloenzymes allow for such complex chemical processes, as they catalyze a myriad of biochemical reactions both efficiently and selectively, where the metal cofactor provides additional functionality to promote reactivity not readily achieved in their absence. While the past 60 years have yielded considerable insight on how enzymes catalyze these reactions, a need to engineer and develop artificial metalloenzymes has been driven not only by industrial and therapeutic needs, but also by innate human curiosity. The design of miniature enzymes, both rationally and through serendipity, using both organic and inorganic building blocks has been explored by many scientists over the years and significant progress has been made. Herein, recent developments over the past 5 years in areas that have not been recently reviewed are summarized, and prospects for future research in these areas are addressed.

An artificial metalloenzyme biosensor can detect ethylene gas in fruits and Arabidopsis leaves.

Enzyme biosensors are useful tools that can monitor rapid changes in metabolite levels in real-time. However, current approaches are largely constrained to metabolites within a limited chemical space. With the rising development of artificial metalloenzymes (ArM), a unique opportunity exists to design biosensors from the ground-up for metabolites that are difficult to detect using current technologies. Here we present the design and development of the ArM ethylene probe (AEP), where an albumin scaffold is used to solubilize and protect a quenched ruthenium catalyst. In the presence of the phytohormone ethylene, cross metathesis can occur to produce fluorescence. The probe can be used to detect both exogenous- and endogenous-induced changes to ethylene biosynthesis in fruits and leaves. Overall, this work represents an example of an ArM biosensor, designed specifically for the spatial and temporal detection of a biological metabolite previously not accessible using enzyme biosensors.

Aliivibrio wodanis as a production host: development of genetic tools for expression of cold-active enzymes.

BACKGROUND: Heterologous production of cold-adapted proteins currently represents one of the greatest bottlenecks in the ongoing bioprospecting efforts to find new enzymes from low-temperature environments, such as, the polar oceans that represent essentially untapped resources in this respect. In mesophilic expression hosts such as Escherichia coli, cold-adapted enzymes often form inactive aggregates. Therefore it is necessary to develop new low-temperature expression systems, including identification of new host organisms and complementary genetic tools. Psychrophilic bacteria, including Pseudoalteromonas haloplanktis, Shewanella and Rhodococcus erythropolis have all been explored as candidates for such applications. However to date none of these have found widespread use as efficient expression systems, or are commercially available. In the present work we explored the use of the sub-Arctic bacterium Aliivibrio wodanis as a potential host for heterologous expression of cold-active enzymes. RESULTS: We tested 12 bacterial strains, as well as available vectors, promoters and reporter systems. We used RNA-sequencing to determine the most highly expressed genes and their intrinsic promoters in A. wodanis. In addition we examined a novel 5'-fusion to stimulate protein production and solubility. Finally we tested production of a set of "difficult-to-produce" enzymes originating from various bacteria and one Archaea. Our results show that cold-adapted enzymes can be produced in soluble and active form, even in cases when protein production failed in E. coli due to the formation of inclusion bodies. Moreover, we identified a 60-bp/20-aa fragment from the 5'-end of the AW0309160_00174 gene that stimulates expression of Green Fluorescent Protein and improves production of cold-active enzymes when used as a 5'-fusion. A 25-aa peptide from the same protein enhanced secretion of a 25-aa-sfGFP fusion. CONCLUSIONS: Our results indicate the use of A. wodanis and associated genetic tools for low-temperature protein production and indicate that A. wodanis represents an interesting platform for further development of a protein production system that can promote further cold-enzyme discoveries.

Protecting Enzymes from Stress-Induced Inactivation.

The pharmaceutical and chemical industries depend on additives to protect enzymes and other proteins against stresses that accompany their manufacture, transport, and storage. Common stresses include vacuum-drying, freeze-thawing, and freeze-drying. The additives include sugars, compatible osmolytes, amino acids, synthetic polymers, and both globular and disordered proteins. Scores of studies have been published on protection, but the data have never been analyzed systematically. To spur efforts to understand the sources of protection and ultimately develop more effective formulations, we review ideas about the mechanisms of protection, survey the literature searching for patterns of protection, and then compare the ideas to the data.

A Synthetic Model of Enzymatic [Fe4S4]-Alkyl Intermediates.

Although alkyl complexes of [Fe4S4] clusters have been invoked as intermediates in a number of enzymatic reactions, obtaining a detailed understanding of their reactivity patterns and electronic structures has been difficult owing to their transient nature. To address this challenge, we herein report the synthesis and characterization of a 3:1 site-differentiated [Fe4S4]2+-alkyl cluster. Whereas [Fe4S4]2+ clusters typically exhibit pairwise delocalized electronic structures in which each Fe has a formal valence of 2.5+, Mössbauer spectroscopic and computational studies suggest that the highly electron-releasing alkyl group partially localizes the charge distribution within the cubane, an effect that has not been previously observed in tetrahedrally coordinated [Fe4S4] clusters.

Semisynthesis of an Active Enzyme by Quantitative Click Ligation.

The incorporation of clickable noncanonical amino acids (ncAAs) has proven to an invaluable tool in chemical biology and protein science research. Nevertheless, the number of examples in which the method is used for preparative purposes is extremely limited. We report the synthesis of an active enzyme by quantitative, Cu(I)-catalyzed ligation of two inactive protein halves, expressed and equipped with an azide and alkyne moiety, respectively, through ncAA incorporation. The reported quantitative conversion is exceptional given the large size of the protein fragments and the fact that no linker or excess of either of the polypeptides was used. The triazole bridge formed between the ncAA side chains was shown to effectively mimic a natural protein loop, providing an enzyme with the same activity as its natural counterpart. We envision that this strategy, termed split-click protein chemistry, can be used for the production of proteins that are difficult to express as full-length entities. It also paves the way for the design of new proteins with tailor-made functionalities.

Biomineralization Synthesis of the Cobalt Nanozyme in SP94-Ferritin Nanocages for Prognostic Diagnosis of Hepatocellular Carcinoma.

Nanomaterials with intrinsic enzyme-like activities (nanozymes) have emerged as promising agents for cancer theranostics strategies. However, size-controllable synthesis of nanozymes and their targeting modifications are still challenging. Here, we report a monodispersed ferritin-based cobalt nanozyme (HccFn(Co3O4)) that specifically targets and visualizes clinical hepatocellular carcinoma (HCC) tissues. The cobalt nanozyme is biomimetically synthesized within the protein shell of the HCC-targeted ferritin (HccFn) nanocage, which is enabled by the display of HCC cell-specific peptide SP94 on the surface of ferritin through a genetic engineering approach. The intrinsic peroxidase-like activity of HccFn(Co3O4) nanozymes catalyzes the substrates to make color reaction to visualize HCC tumor tissues. We examined 424 clinical HCC specimens and verified that HccFn(Co3O4) nanozymes distinguish HCC tissues from normal liver tissues with a sensitivity of 63.5% and specificity of 79.1%, which is comparable with that of the clinically used HCC-specific marker α fetoprotein. Moreover, the pathological analysis indicates that the HccFn(Co3O4) nanozyme staining result is a potential predictor of prognosis in HCC patients. Staining intensity is positively correlated to tumor differentiation degree ( P = 0.0246) and tumor invasion ( P < 0.0001) and negatively correlated with overall survival ( P = 0.0084) of HCC patients. Together, our study demonstrates that ferritin is an excellent platform for size-controllable synthesis and targeting modifications of nanozymes, and the HccFn(Co3O4) nanozyme is a promising reagent for prognostic diagnosis of HCC.

The first protection-free synthesis of magnetic bifunctional l-proline as a highly active and versatile artificial enzyme: Synthesis of imidazole derivatives.

l-Proline is a bifunctional versatile organocatalyst that could promote a variety of useful transformations. Some passive and dynamic interactions between this simple amino acid and different substrates, which are necessary to enzymatic reactions, have given it "the simplest enzyme" title. Herein we presented the first report on the synthesis of magnetic bifunctional l-proline as an artificial enzyme without requiring any protection/deprotection steps according to an operationally simple process. This magnetic nano-biocatalyst is a promising catalyst that in a case study was successfully applied for the synthesis of 2,4,5-trisubstituted and 1,2,4,5-tetrasubstituted imidazoles in the 70-99% and 60-90% yields respectively, which it could be extended to the variety of l-proline-based organic transformations. The synergic effect of bifunctional l-proline shell as catalytic active site and magnetite nanoparticles core, which could function as protein mimics endow it high efficiency, versatility, recoverability, reusability and good turnover frequency, which are necessary characters for artificial enzymes' designing.

Self-Assembled Peptide-Carbon Nitride Hydrogel as a Light-Responsive Scaffold Material.

Peptide self-assembly is a facile route to the development of bioorganic hybrid materials that have sophisticated nanostructures toward diverse applications. Here, we report the synthesis of self-assembled peptide (Fmoc-diphenylalanine, Fmoc-FF)/graphitic carbon nitride (g-C3N4) hydrogels for light harvesting and biomimetic photosynthesis through noncovalent interactions between aromatic rings in Fmoc-FF nanofibers and tris-s-triazine in g-C3N4 nanosheets. According to our analysis, the photocurrent density of the Fmoc-FF/g-C3N4 hydrogel was 1.8× higher (0.82 µA cm-1) than that of the pristine g-C3N4. This is attributed to effective exfoliation of g-C3N4 nanosheets in the Fmoc-FF/g-C3N4 network, facilitating photoinduced electron transfers. The Fmoc-FF/g-C3N4 hydrogel reduced NAD+ to enzymatically active NADH under light illumination at a high rate of 0.130 mol g-1 h-1 and drove light-responsive redox biocatalysis. Moreover, the Fmoc-FF/g-C3N4 scaffold could well-encapsulate key photosynthetic components, such as electron mediators, cofactors, and enzymes, without noticeable leakage, while retaining their functions within the hydrogel. The prominent activity of the Fmoc-FF/g-C3N4 hydrogel for biomimetic photosynthesis resulted from the easy transfer of photoexcited electrons from electron donors to NAD+ via g-C3N4 and electron mediators as well as the hybridization of key photosynthetic components in a confined space of the nanofiber network.

Exploiting non-covalent π interactions for catalyst design.

Molecular recognition, binding and catalysis are often mediated by non-covalent interactions involving aromatic functional groups. Although the relative complexity of these so-called π interactions has made them challenging to study, theory and modelling have now reached the stage at which we can explain their physical origins and obtain reliable insight into their effects on molecular binding and chemical transformations. This offers opportunities for the rational manipulation of these complex non-covalent interactions and their direct incorporation into the design of small-molecule catalysts and enzymes.

A metal ion regulated artificial metalloenzyme.

Regulation of enzyme activity is essential in living cells. The rapidly increasing number of designer enzymes with new-to-nature activities makes it necessary to develop novel strategies for controlling their catalytic activity. Here we present the development of a metal ion regulated artificial metalloenzyme created by combining two anchoring strategies, covalent and supramolecular, for introducing a regulatory and a catalytic site, respectively. This artificial metalloenzyme is activated in the presence of Fe2+ ions, but only marginally in the presence of Zn2+.

Synthetic biology of modular proteins.

The evolution of natural modular proteins and domain swapping by protein engineers have shown the disruptive potential of non-homologous recombination to create proteins with novel functions or traits. Bacteriophage endolysins, cellulosomes and polyketide synthases are 3 examples of natural modular proteins with each module having a dedicated function. These modular architectures have been created by extensive duplication, shuffling of domains and insertion/deletion of new domains. Protein engineers mimic these natural processes in vitro to create chimeras with altered properties or novel functions by swapping modules between different parental genes. Most domain swapping efforts are realized with traditional restriction and ligation techniques, which become particularly restrictive when either a large number of variants, or variants of proteins with multiple domains have to be constructed. Recent advances in homology-independent shuffling techniques increasingly address this need, but to realize the full potential of the synthetic biology of modular proteins a complete homology-independent method for both rational and random shuffling of modules from an unlimited number of parental genes is still needed.

Method for Enzyme Design with Genetically Encoded Unnatural Amino Acids.

We describe the methodologies for the design of artificial enzymes with genetically encoded unnatural amino acids. Genetically encoded unnatural amino acids offer great promise for constructing artificial enzymes with novel activities. In our studies, the designs of artificial enzyme were divided into two steps. First, we considered the unnatural amino acids and the protein scaffold separately. The scaffold is designed by traditional protein design methods. The unnatural amino acids are inspired by natural structure and organic chemistry methods, and synthesized by either organic chemistry methods or enzymatic conversion. With the increasing number of published unnatural amino acids with various functions, we described an unnatural amino acids toolkit containing metal chelators, redox mediators, and click chemistry reagents. These efforts enable a researcher to search the toolkit for appropriate unnatural amino acids for the study, rather than design and synthesize the unnatural amino acids from the beginning. After the first step, the model enzyme was optimized by computational methods and directed evolution. Lastly, we describe a general method for evolving aminoacyl-tRNA synthetase and expressing unnatural amino acids incorporated into a protein.

Periplasmic Screening for Artificial Metalloenzymes.

Artificial metalloenzymes represent an attractive means of combining state-of-the-art transition metal catalysis with the benefits of natural enzymes. Despite the tremendous recent progress in this field, current efforts toward the directed evolution of these hybrid biocatalysts mainly rely on the laborious, individual purification of protein variants rendering the throughput, and hence the outcome of these campaigns feeble. We have recently developed a screening platform for the directed evolution of artificial metalloenzymes based on the streptavidin-biotin technology in the periplasm of the Gram-negative bacterium Escherichia coli. This periplasmic compartmentalization strategy comprises a number of compelling advantages, in particular with respect to artificial metalloenzymes, which lead to a drastic increase in the throughput of screening campaigns and additionally are of unique value for future in vivo applications. Therefore, we highlight here the benefits of this strategy and intend to propose a generalized guideline for the development of novel transition metal-based biocatalysts by directed evolution in order to extend the natural enzymatic repertoire.

Construction of an Immobilized Thermophilic Esterase on Epoxy Support for Poly(ε-caprolactone) Synthesis.

Developing an efficient immobilized enzyme is of great significance for improving the operational stability of enzymes in poly(ε-caprolactone) synthesis. In this paper, a thermophilic esterase AFEST from the archaeon Archaeoglobus fulgidus was successfully immobilized on the epoxy support Sepabeads EC-EP via covalent attachment, and the immobilized enzyme was then employed as a biocatalyst for poly(ε-caprolactone) synthesis. The enzyme loading and recovered activity of immobilized enzyme was measured to be 72 mg/g and 10.4 U/mg using p-nitrophenyl caprylate as the substrate at 80 °C, respectively. Through the optimization of reaction conditions (enzyme concentration, temperature, reaction time and medium), poly(ε-caprolactone) was obtained with 100% monomer conversion and low number-average molecular weight (Mn < 1300 g/mol). Further, the immobilized enzyme exhibited excellent reusability, with monomer conversion values exceeding 75% during 15 batch reactions. Finally, poly(ε-caprolactone) was enzymatically synthesized with an isolated yield of 75% and Mn value of 3005 g/mol in a gram-scale reaction.

Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches.

This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.