Protein-inorganic calcium-phosphate supraparticles as a robust platform for enzyme co-immobilization

Biocatalytic reductive aminations with NAD(P)H-dependent enzymes: enzyme discovery, engineering and synthetic applications

Chiral amines are pivotal building blocks for the pharmaceutical industry. Asymmetric reductive amination is one of the most efficient and atom economic methodologies for the synthesis of optically active amines. Among the various strategies available, NAD(P)H-dependent amine dehydrogenases (AmDHs) and imine reductases (IREDs) are robust enzymes that are available from various sources and capable of utilizing a broad range of substrates with high activities and stereoselectivities. AmDHs and IREDs operate via similar mechanisms, both involving a carbinolamine intermediate followed by hydride transfer from the co-factor. In addition, both groups catalyze the formation of primary and secondary amines utilizing both organic and inorganic amine donors. In this review, we discuss advances in developing AmDHs and IREDs as biocatalysts and focus on evolutionary history, substrate scope and applications of the enzymes to provide an outlook on emerging industrial biotechnologies of chiral amine production.

Non-covalent binding tags for batch and flow biocatalysis

Enzyme immobilization offers considerable advantage for biocatalysis in batch and continuous flow reactions. However, many currently available immobilization methods require that the surface of the carrier is chemically modified to allow site specific interactions with their cognate enzymes, which requires specific processing steps and incurs associated costs. Two carriers (cellulose and silica) were investigated here, initially using fluorescent proteins as models to study binding, followed by assessment of industrially relevant enzyme performance (transaminases and an imine reductase/glucose oxidoreductase fusion). Two previously described binding tags, the 17 amino acid long silica-binding peptide from the Bacillus cereus CotB protein and the cellulose binding domain from the Clostridium thermocellum, were fused to a range of proteins without impairing their heterologous expression. When fused to a fluorescent protein both tags conferred high avidity specific binding with their respective carriers (low nanomolar K_d values). The CotB peptide (CotB1p) induced protein aggregation in the transaminase and imine reductase/glucose oxidoreductase fusions when incubated with the silica carrier. The Clostridium thermocellum cellulose binding domain (CBDclos) allowed immobilization of all the proteins tested, but immobilization led to loss of enzymatic activity in the transaminases (< 2-fold) and imine reductase/glucose oxidoreductase fusion (> 80%). A transaminase-CBDclos fusion was then successfully used to demonstrate the application of the binding tag in repetitive batch and a continuous-flow reactor.

Self-Assembly of Functional Protein Nanosheets from Thermoresponsive Bolaamphiphiles

Nanosheets are two-dimensional materials, less than 100 nm thick, that can be used for separations, biosensing, and biocatalysis. Nanosheets can be made from inorganic and organic materials such as graphene, polymers, and proteins. Here, we report the self-assembly of nanosheets under aqueous conditions from functional proteins. The nanosheets are synthesized from two fusion proteins held together by high-affinity interactions of two leucine zippers to form bolaamphiphiles. The hydrophobic domain, Z_R-ELP-Z_R, contains the thermoresponsive elastin-like peptide (ELP) flanked by arginine-rich leucine zippers (Z_R), each of which binds the hydrophilic fusion protein, globule-Z_E, via the glutamate-rich leucine zipper (Z_E) fused to a functional, globular protein. Nanosheets form when the proteins are mixed at 4 °C in aqueous solutions and then heated to 25 °C as the container is rotated end-over-end causing expansion and contraction of the air-water interface. The nanosheets are robust with respect to the choice of globular protein and can incorporate small fluorescent proteins that are less than 30 kDa as well as large enzymes, such as 80 kDa malate synthase G. Upon incorporation into nanosheets, enzymes retain more than 70% of their original activity, demonstrating the potential of protein nanosheets to be used for biosensing or biocatalytic applications.

Protein Mediated Enzyme Immobilization

Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.

Heterogeneous Synthetic Vesicles toward Artificial Cells: Engineering Structure and Composition of Membranes for Multimodal Functionalities

The desire to develop artificial cells to imitate living cells in synthetic vesicle platforms has continuously increased over the past few decades. In particular, heterogeneous synthetic vesicles made from two or more building blocks have attracted attention for artificial cell applications based on their multifunctional modules with asymmetric structures. In addition to the traditional liposomes or polymersomes, polypeptides and proteins have recently been highlighted as potential building blocks to construct artificial cells owing to their specific biological functionalities. Incorporating one or more functionally folded, globular protein into synthetic vesicles enables more cell-like functions mediated by proteins. This Review highlights the recent research about synthetic vesicles toward artificial cell models, from traditional synthetic vesicles to protein-assembled vesicles with asymmetric structures. We aim to provide fundamental and practical insights into applying knowledge on molecular self-assembly to the bottom-up construction of artificial cell platforms with heterogeneous building blocks.

Leloir glycosyltransferases enabled to flow synthesis: Continuous production of the natural C-glycoside nothofagin

C‐glycosyltransferase (CGT) and sucrose synthase (SuSy), each fused to the cationic binding module Z_basic2, were co‐immobilized on anionic carrier (ReliSorb SP400) and assessed for continuous production of the natural C‐glycoside nothofagin. The overall reaction was 3ʹ‐C‐β‐glycosylation of the polyphenol phloretin from uridine 5ʹ‐diphosphate (UDP)‐glucose that was released in situ from sucrose and UDP. Using solid catalyst optimized for total (∼28 mg/g) as well as relative protein loading (CGT/SuSy = ∼1) and assembled into a packed bed (1 ml), we demonstrate flow synthesis of nothofagin (up to 52 mg/ml; 120 mM) from phloretin (≥95% conversion) solubilized by inclusion complexation in hydroxypropyl β‐cyclodextrin. About 1.8 g nothofagin (90 ml; 12–26 mg/ml) were produced continuously over 90 reactor cycles (2.3 h/cycle) with a space‐time yield of approximately 11 mg/(ml h) and a total enzyme turnover number of up to 2.9 × 10³ mg/mg (=3.8 × 10⁵ mol/mol). The co‐immobilized enzymes exhibited useful effectiveness (∼40% of the enzymes in solution), with limitations on the conversion rate arising partly from external liquid–solid mass transfer of UDP under packed‐bed flow conditions. The operational half‐life of the catalyst (∼200 h; 30°C) was governed by the binding stability of the glycosyltransferases (≤35% loss of activity) on the solid carrier. Collectively, the current study shows integrated process technology for flow synthesis with co‐immobilized sugar nucleotide‐dependent glycosyltransferases, using efficient glycosylation from sucrose via the internally recycled UDP‐glucose. This provides a basis from engineering science to promote glycosyltransferase applications for natural product glycosides and oligosaccharides.

Tuning the Morphology of Protein-Inorganic Calcium-Phosphate Supraparticles via Directed Assembly

Understanding the phenomena that govern complex interfacial and directed assemblies is essential for both control and scale-up of particle syntheses. The present work describes an effort to understand, control, and tune the formation of protein-inorganic calcium-phosphate supraparticles that are produced at an oscillating air-water interface created by end-over-end rotation of the synthesis solution. Supraparticles were synthesized under an array of different conditions that varied reagent concentration, the presence of additives, tube size, and rotational speed. Paired with a fluid mechanics model of the end-over-end rotation and dimensional analysis, the sensitivity of the synthesis to physicochemical and mechanical parameters was determined. Surface tension and bubble formation were found to be important criteria for changing the size distribution of supraparticles. Thresholds for the values of the Froude, Iribarren, and rotational Reynolds numbers were identified for narrowing particle size distribution. These results both guide the specific protein-inorganic supraparticle synthesis described here and inform future manipulation and scale-up of other complex interfacial colloidal assemblies.

Novel Bionanocompounds: Outer Membrane Protein A and Lacasse Co-Immobilized on Magnetite Nanoparticles for Produced Water Treatment

The oil and gas industry generates large amounts of oil-derived effluents such as Heavy Crude Oil (HCO) in water (W) emulsions, which pose a significant remediation and recovery challenge due to their high stability and the presence of environmentally concerning compounds. Nanomaterials emerge as a suitable alternative for the recovery of such effluents, as they can separate them under mild conditions. Additionally, different biomolecules with bioremediation and interfacial capabilities have been explored to functionalize such nanomaterials to improve their performance even further. Here, we put forward the notion of combining these technologies for the simultaneous separation and treatment of O/W effluent emulsions by a novel co-immobilization approach where both OmpA (a biosurfactant) and Laccase (a remediation enzyme) were effectively immobilized on polyether amine (PEA)-modified magnetite nanoparticles (MNPs). The obtained bionanocompounds (i.e., MNP-PEA-OmpA, MNP-PEA-Laccase, and MNP-PEA-OmpA-Laccase) were successfully characterized via DLS, XRD, TEM, TGA, and FTIR. The demulsification of O/W emulsions was achieved by MNP-PEA-OmpA and MNP-PEA-OmpA-Laccase at 5000 ppm. This effect was further improved by applying an external magnetic field to approach HCO removal efficiencies of 81% and 88%, respectively. The degradation efficiencies with these two bionanocompounds reached levels of between 5% and 50% for the present compounds. Taken together, our results indicate that the developed nanoplatform holds significant promise for the efficient treatment of emulsified effluents from the oil and gas industry.

Tuning the Structural Integrity and Mechanical Properties of Globular Protein Vesicles by Blending Crosslinkable and NonCrosslinkable Building Blocks

Vesicles made from functionally folded, globular proteins that perform specific biological activities, such as catalysis, sensing, or therapeutics, show potential applications as artificial cells, microbioreactors, or protein drug delivery vehicles. The mechanical properties of vesicle membranes, including the elastic modulus and hardness, play a critical role in dictating the stability and shape transformation of the vesicles under external stimuli triggers. Herein, we have developed a strategy to tune the mechanical properties and integrity of globular protein vesicle (GPV) membranes of which building molecules are recombinant fusion protein complexes: a mCherry fused with an acidic leucine zipper (mCherry-Z_E) and a basic leucine zipper fused with an elastin-like polypeptide (Z_R-ELP). To control the mechanical properties of GPVs, we introduced a nonstandard amino acid (para-azidophenylalanine (pAzF)) into the ELP domains (ELP-X), which enabled the creation of crosslinked vesicles under ultraviolet (UV) irradiation. Crosslinked GPVs made from mCherry-Z_E/Z_R-ELP-X complexes presented higher stability than noncrosslinked GPVs under hypotonic osmotic stress. The degree of swelling of GPVs increased as less crosslinking was achieved in the vesicle membranes, which resulted in the disassembly of GPVs into membraneless coacervates. Nanoindentation by atomic force microscopy (AFM) confirmed that the stiffness and Young's elastic modulus of GPVs increase as the blending molar ratio of Z_R-ELP-X to Z_R-ELP increases to make vesicles. The results obtained in this study suggest a rational design to make GPVs with tunable mechanical properties for target applications by simply varying the blending ratio of Z_R-ELP and Z_R-ELP-X in the vesicle self-assembly.

Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.