Magnetic Nanoplatforms for Covalent Protein Immobilization Based on Spy Chemistry

Protein Immobilization Inspired Lysosomal Disruption for Efficient Nuclear Drug Delivery

The high metabolism and excessive growth of tumor cells result in the development of a tumor microenvironment (TME) and enhanced lysosomal activity within the cells, which can eliminate chemotherapeutics. Consequently, the design of nanocarriers that respond to TME and target tumor cell lysosomes represents an optimal strategy to enhance drug specificity and utilization efficiency. Herein, inspired by protein immobilization, a dual-responsive supramolecular nanomedicine FPA/DOX is developed for specifically targeting the TME and tumor cell lysosomes. Upon hypoxia and acidic response, FPA/DOX exposes benzaldehyde groups that engage with amino groups on lysosomal proteins by protein covalent immobilization reaction─an imidization condensation reaction, leading to protein denaturation and inactivation and inducing lysosomal membrane permeabilization (LMP). This LMP process not only triggers lysosomal-dependent cell death (LDCD) but also facilitates the rapid translocation of released DOX into the cell nucleus. In vitro experiments have demonstrated that the tumor cell toxicity of FPA/DOX is 4.2 times that of free DOX. Additionally, in vivo studies have verified the high biosafety of FPA/DOX, with a remarkable tumor inhibition rate of 95.27%. In summary, the lysosomal disruption inspired by protein immobilization has pioneered an approach for tumor treatment and holds great potential in biomedical applications.

A novel Affi-Cova magnetic nanoparticles for one-step covalent immobilization of His-tagged enzyme directly from crude cell lysate

Owing to the rapid advancement of in vitro synthetic biology, functional carriers capable of covalently binding target proteins from crude lysates under mild conditions have garnered escalating attention. Herein, a magnetic nanoparticle with affinity/covalent bifunction (MNP@Affi-Cova) was developed for the direct covalent immobilization of the recombinant enzyme of His-tagged birA (r-birA) from crude cell lysates in a single step. This innovative approach is attributed to the presence of chelated Ni2+ ions and epoxy groups on the surface of the beads. The fabricated magnetic nanoparticles were characterized by SEM, FT-IR spectrum, and zeta potential. The application conditions and stability of the MNP@Affi-Cova beads were systematically evaluated. Notably, the MNP@Affi-Cova beads exhibited a covalent capture efficiency of 91.25 μg r-birA/mg beads from a cell lysate supernatant containing 2.62 mg/mL crude protein. The immobilized r-birA exhibited significantly enhanced pH and thermal stability compared to the free counterpart. Additionally, the reusability of the immobilized r-birA on MNP@Affi-Cova demonstrated the retention of 76.1 % of its initial activity over ten cycles. These results suggest that the MNP@Affi-Cova presents considerable potential as a support for the covalent immobilization of recombinant His-tagged enzymes directly from crude lysates, thereby circumventing the labor-intensive purification process typically required before enzyme immobilization.

A Versatile Magnetic Nanoplatform for Plug-and-Play Functionalization: Genetically Programmable Cargo Loading to Bacterial Magnetosomes by SpyCatcher "Click Biology"

Bacterial magnetosomes ("MAGs") represent a promising class of magnetic iron oxide nanoparticles with exceptional material characteristics and high application potential in the biomedical and biotechnological field. For the surface functionalization of MAGs with different protein cargos, their enveloping membrane can be addressed by genetic means. However, the expression of foreign polypeptides as translational fusion to magnetosome membrane proteins is still laborious and lacks versatility as the generated particles are monospecific and thus restricted to predetermined functions. Utilizing the SpyTag-SpyCatcher (ST-SC) bioconjugate system, we here establish a flexible platform for the targeted nanoassembly of multifunctional MAGs that combines the rapidity of chemical coupling (e.g., by cross-linking reactions) and the unmatched selectivity and controllability of in vivo functionalization. MAGs genetically engineered to display either SC- or ST-connectors are shown to efficiently bind a variety of complementary tagged (protein) cargo. Specifically, we cover a broad spectrum of representative functional moieties and foreign cargo (such as enzymes, antibodies, fluorophores, and silica beads) with relevance in biotechnology and biomedicine and demonstrate the interchangeability of the MAGs-adapted ST-SC system. For the controlled generation of artificial shells surrounding the particles, SC-MAGs are effectively coated by protein-corona proteins. The potential of the here-provided toolkit is even more enhanced by using SC-MAGs as an affinity tool for selective protein pulldown in vitro and in vivo. Overall, this innovative technology turns bacterial MAGs into a flexible magnetic nanoscaffold for the targeted plug-and-play display of virtually unlimited additional functionalities, thereby generating a multitude of magnetic hybrid materials that can be used in many applications.

Protein-polymer bioconjugation, immobilization, and encapsulation: a comparative review towards applicability, functionality, activity, and stability

Polymer-based biomaterials have received a lot of attention due to their biomedical, agricultural, and industrial potential. Soluble protein-polymer bioconjugates, immobilized proteins, and encapsulated proteins have been shown to tune enzymatic activity, improved pharmacokinetic ability, increased chemical and thermal stability, stimuli responsiveness, and introduced protein recovery. Controlled polymerization techniques, increased protein-polymer attachment techniques, improved polymer surface grafting techniques, controlled polymersome self-assembly, and sophisticated characterization methods have been utilized for the development of well-defined polymer-based biomaterials. In this review we aim to provide a brief account of the field, compare these methods for engineering biomaterials, provide future directions for the field, and highlight impacts of these forms of bioconjugation.

Engineering biomaterials for the recovery of rare earth elements

The escalating global demand for rare earth elements (REEs) and the overabundance of REE-containing waste require innovative technologies for REE recovery from waste to achieve a sustainable supply of REEs while reducing the environmental burden. Biosorption mediated by peptides or proteins has emerged as a promising approach for selective REE recovery. To date, multiple peptides and proteins with high REE-binding affinity and selectivity have been discovered, and various strategies are being exploited to engineer robust and reusable biosorptive materials for selective REE recovery. This review highlights recent advances in discovering and engineering peptides and proteins for REE recovery. Future research prospects and challenges are also discussed.

Site-directed immobilization of enzymes on nanoparticles using self-assembly systems

Enzyme immobilization is an effective method for improving the stability and reusability. However, linking at random sites on the enzyme results in low catalytic efficiency due to blockage of the active site or conformational changes. Therefore, controlling the orientation of enzymes on the carrier has been developed. Here, the site-specific mutation and the SpyTag/SpyCatcher systems were used to prepare a site-directed immobilized enzyme. The thermal stability of the immobilized enzyme was better than that of the free enzyme, and ≥80 % of the catalytic activity was retained after 30 days of storage. Furthermore, the Michaelis constant (Km) and the turnover number (kcat) of the immobilized enzyme were 5.23-fold lower and 6.11-fold higher than those of the free enzyme, respectively, which appeared to be related to changes in secondary structure after immobilization. These findings provide a new and effective option for enzyme-directed immobilization.

Spontaneous and site-specific immobilization of PNGase F via spy chemistry

Protein N-glycosylation plays a critical role in a wide range of biological processes, and aberrant N-glycosylation is frequently associated with various pathological states. For global N-glycosylation analysis, N-glycans are typically released from glycoproteins mediated by endoglycosidases, primarily peptide N-glycosidase F (PNGase F). However, conventional N-glycan release by in-solution PNGase F is time-consuming and nonreusable. Although some immobilization methods can save time and reduce the enzyme dosage, including affinity interaction and covalent binding, the immobilized PNGase F by these traditional methods may compromises the immobilized enzyme's stability and biofunction. Therefore, a new approach is urgently needed to firmly and steadily immobilize PNGase F. To meet this demand, we have developed a spontaneous and site-specific way to immobilize PNGase F onto magnetic nanoparticles via Spy chemistry. The magnetic nanoparticles were synthesized and modified with SpyTag as a solid surface. The PNGase F fused with SpyCatcher can then be site-specifically and covalently immobilized onto this solid phase, forming a firm isopeptide bond via self-catalysis between the SpyTag peptide and SpyCatcher. Importantly, the immobilization process mediated by mild spy chemistry does not result in PNGase F inactivation; and allows immobilized PNGase F to rapidly release various types of glycans (high-mannose, sialylated, and hybrid) from glycoproteins. Moreover, the immobilized PNGase F exhibited good deglycosylation activity and facilitated good reusability in consecutive reactions. Deglycosylation of clinical samples was completed by the immobilized PNGase F as fast as several minutes.

Modification of bacterial microcompartments with target biomolecules via post-translational SpyTagging

Bacterial microcompartments (BMCs) are proteinaceous organelle-like structures formed within bacteria, often encapsulating enzymes and cellular processes, in particular, allowing toxic intermediates to be shielded from the general cellular environment. Outside of their biological role they are of interest, through surface modification, as potential drug carriers and polyvalent antigen display scaffolds. Here we use a post-translational modification approach, using copper free click chemistry, to attach a SpyTag to a target protein molecule for attachment to a specific SpyCatcher modified BMC shell protein. We demonstrate that a post-translationally SpyTagged material can react with a SpyCatcher modified BMC and show its presence on the surface of BMCs, enabling future investigation of these structures as polyvalent antigen display scaffolds for vaccine development. This post-translational 'click' methodology overcomes the necessity to genetically encode the SpyTag, avoids any potential reduction in expression yield and expands the scope of SpyTag/SpyCatcher vaccine scaffolds to form peptide epitope vaccines and small molecule delivery agents.

Boronic Acid Resin for Selective Immobilization of Canonically Encoded Proteins

The use of transition-metal-mediated boronic acid chemistry presents a novel method of protein immobilization on a solid support. This is a one-step method that site-selectively immobilizes pyroglutamate-histidine (pGH)-tagged proteins. Herein, we describe the synthesis of alkenylboronic acid-functionalized poly(ethylene glycol) acrylamide (PEGA) resin and its subsequent reactions with pGH-tagged proteins to produce covalent linkages. The selectivity of immobilization is demonstrated within fluorescent studies, model mixtures, and lysates.

Rapid, Direct, Noninvasive Method to Determine the Amount of Immobilized Protein

Protein immobilization is of utmost importance in many areas, where various proteins are used for selective detection of target compounds. Despite the importance given to determine the amount of immobilized protein, there is no simple method that allows direct, noninvasive detection. In this work, a method based on pH transition, occurring during change of solution ionic strength, was developed. The method utilized the ionic character of the immobilized protein while implementing biologically compatible buffers. Five different proteins, namely, glucose oxidase, horseradish peroxidase, bovine serum albumin, lysozyme, and protein A, were immobilized in different amounts on a porous polymeric matrix, and their pH transition was measured using lactate buffer of various concentrations and pH values. A linear correlation was found between the amount of immobilized protein and the amplitude of the pH transition, allowing the detection down to 2 nmol of immobilized protein. By changing the buffer concentration and pH, the sensitivity of the method could be tailored. Criteria based on the symmetry of the pH transition peak have been developed to determine if a particular measurement is within a linear range. In addition, a mathematical model was developed enabling prediction of pH transition profiles based solely on the protein amino acid sequence, the buffer pK_a value(s), and the amount of immobilized protein.Hence, it can be used to design pH transition method experiments to achieve the required sensitivity for a target sample. Since the proposed method is noninvasive, it can be routinely applied during optimization of the immobilization protocol, for quality control, and also as an in-process monitoring tool.

Lanmodulin-Functionalized Magnetic Nanoparticles as a Highly Selective Biosorbent for Recovery of Rare Earth Elements

Recovering rare earth elements (REEs) from waste streams represents a sustainable approach to diversify REE supply while alleviating the environmental burden. However, it remains a critical challenge to selectively separate and concentrate REEs from low-grade waste streams. In this study, we developed a new type of biosorbent by immobilizing Lanmodulin-SpyCatcher (LanM-Spycatcher) on the surface of SpyTag-functionalized magnetic nanoparticles (MNPs) for selective separation and recovery of REEs from waste streams. The biosorbent, referred to as MNP-LanM, had an adsorption activity of 6.01 ± 0.11 μmol-terbium/g-sorbent and fast adsorption kinetics. The adsorbed REEs could be desorbed with >90% efficiency. The MNP-LanM selectively adsorbed REEs in the presence of a broad range of non-REEs. The protein storage stability of the MNP-LanM increased by two-fold compared to free LanM-SpyCatcher. The MNP-LanM could be efficiently separated using a magnet and reused with high stability as it retained ∼95% of the initial activity after eight adsorption-desorption cycles. Furthermore, the MNP-LanM selectively adsorbed and concentrated REEs from the leachate of coal fly ash and geothermal brine, resulting in 967-fold increase of REE purity. This study provides a scientific basis for developing innovative biosorptive materials for selective and efficient separation and recovery of REEs from low-grade feedstocks.

Biomimetic one-pot preparation of surface biofunctionalized silica-coated magnetic composites for dual enzyme oriented immobilization without pre-purification

Surface functioned magnetic silica particles are efficient carriers to achieve facilitated separation and recycling of biocatalysts. However, traditional methods of modifying magnetic silica particles required time-costly sequential coating and surface modification steps and toxic solvents. Herein, a green and efficient routine was proposed to prepare the surface modified silica-coated magnetic microspheres (SCEs@SiO₂ @Fe₃O₄) in one-pot. The elastin-like polypeptides (ELPs)-SpyCatcher chimera (SCEs) were purified by inverse transition cycling with high yield (275 mg/L) and incorporated into the magnetic silica spheres based on the biomimetic silicification capability of ELPs as proved by the EDS and SEM mapping. No SCEs leaked was observed within 48 h, indicating excellent stability in buffer. Then, the biofunctionalized carriers were used to purify and immobilize the target dual enzymes (xylanase-linker-SpyTag-linker-lichenase, bienzymes) directly from the crude cell lysis solution by the spontaneous isopeptide bond reaction between SpyCatcher and SpyTag. The immobilized bienzymes were sphere-like magnetic silica particles with uniform size, which had good magnetic responsiveness. The immobilization yield, immobilization efficiency and activity recovery for xylanase were 86%, 84 % and 72 %, while for lichenase was 92 %, 86 % and 79 %, respectively. Besides, the immobilized bienzymes showed good reusability (>60 %, 10 times for xylanase, >95 %, 8 times for lichenase). The SCEs modified silica-coated magnetic microspheres are expected to provide versatile platforms for single-step of purification and immobilization of multienzymes, offering great potentials in the field of biocatalysis.

Magnetic Nanoparticles for Protein Separation and Purification

Proteins are essential for various functions such as brain activity and muscle contraction in humans. Even though food is a source of proteins, the bioavailability of proteins in most foods is usually limited due to matrix interaction with other biomolecules. Thus, it is essential to extract these proteins and provide them as a nutraceutical supplement to maintain protein levels and avoid protein deficiency. Hence, protein purification and extraction from natural sources are highly significant in biomedical applications. Chromatography, crude mechanical disruption, use of extractive chemicals, and electrophoresis are some of the methods applied to isolate specific proteins. Even though these methods possess several advantages, they are unable to extract specific proteins with high purity. A suitable alternative is the use of nanoparticles, which can be beneficial in protein purification and extraction. Notably, magnetic iron and iron-based nanoparticles have been employed in protein extraction processes and can be reused via demagnetization due to their magnetic property, smaller size, morphology, high surface-to-volume ratio, and surface charge-mediated property. This chapter is a summary of various magnetic nanoparticles (MNPs) that can be used for the biomolecular separation of proteins.

Site-Specific and Tunable Co-immobilization of Proteins onto Magnetic Nanoparticles via Spy Chemistry

Co-immobilization of multiple proteins onto one nanosupport has large potential in mimicking natural multiprotein complexes and constructing efficient cascade biocatalytic systems. However, control of different proteins regarding their spatial arrangement and loading ratio remains a big challenge, and protein co-immobilization often requires the use of purified proteins. Herein, built upon our recently designed SpyTag-functionalized magnetic nanoparticles (MNPs), we established a modular MNP platform for site-specific, tunable, and cost-effective protein co-immobilization. SpyCatcher-fused enhanced green fluorescent protein (i.e., EGFP-SpyCatcher) and mCherry red fluorescent protein (i.e., RFP-SpyCatcher) were designed and conjugated on MNPs, and the immobilized proteins showed 3-7-fold enhancement in storage stability and greatly improved stability against the freeze-thaw process compared to free proteins. The protein-conjugated MNPs also retained desirable colloidal stability and magnetic responsiveness, enabling facile proteins' recovery. Also, one-pot co-immobilization of the two proteins could be fine-tuned with their feed ratios. In addition, MNPs could selectively and efficiently co-immobilize both SpyCatcher-fused proteins from combined cell lysates without purification, offering a convenient and cost-effective approach for multiprotein immobilization. This MNP platform provides a facile and efficient tool to construct bionano hybrid materials (i.e., protein-based MNPs) and multiprotein systems for a variety of industrial and green chemistry applications.

Fabrication of multifunctional metal-organic frameworks nanoparticles via layer-by-layer self-assembly to efficiently discover PSD95-nNOS uncouplers for stroke treatment

Background

Disruption of the postsynaptic density protein-95 (PSD95)—neuronal nitric oxide synthase (nNOS) coupling is an effective way to treat ischemic stroke, however, it still faces some challenges, especially lack of satisfactory PSD95-nNOS uncouplers and the efficient high throughput screening model to discover them.

Results

Herein, the multifunctional metal–organic framework (MMOF) nanoparticles as a new screening system were innovatively fabricated via layer-by-layer self-assembly in which His-tagged nNOS was selectively immobilized on the surface of magnetic MOF, and then PSD95 with green fluorescent protein (GFP-PSD95) was specifically bound on it. It was found that MMOF nanoparticles not only exhibited the superior performances including the high loading efficiency, reusability, and anti-interference ability, but also possessed the good fluorescent sensitivity to detect the coupled GFP-PSD95. After MMOF nanoparticles interacted with the uncouplers, they would be rapidly separated from uncoupled GFP-PSD95 by magnet, and the fluorescent intensities could be determined to assay the uncoupling efficiency at high throughput level.

Conclusions

In conclusion, MMOF nanoparticles were successfully fabricated and applied to screen the natural actives as potential PSD95-nNOS uncouplers. Taken together, our newly developed method provided a new material as a platform for efficiently discovering PSD95-nNOS uncouplers for stoke treatment.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01583-7.