A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

Engineering Proteins for PEDOT Dispersions: A New Horizon for Highly Mixed Ionic-Electronic Biocompatible Conducting Materials

Poly (3,4-ethylenedioxythiophene) (PEDOT) doped with polystyrene sulfonate (PSS) is the most used conducting polymer from energy to biomedical applications. Despite its exceptional properties, there is a need for developing new materials that can improve some of its inherent limitations, e.g., biocompatibility. In this context, doping PEDOT is propose with a robust recombinant protein with tunable properties, the consensus tetratricopeptide repeated protein (CTPR). The doping consists of an oxidative polymerization, where the PEDOT chains are stabilized by the negative charges of the CTPR protein. CTPR proteins are evaluated with three different lengths (3, 10, and 20 identical CTPR units) and optimized varied synthetic conditions. These findings revealed higher doping rate and oxidized state of the PEDOT chains when doped with the smallest scaffold (CTPR3). These PEDOT:CTPR hybrids possess ionic and electronic conductivity. Notably, PEDOT:CTPR3 displayed an electronic conductivity of 0.016 S cm-1, higher than any other reported protein-doped PEDOT. This result places PEDOT:CTPR3 at the level of PEDOT-biopolymer hybrids, and brings it closer in performance to PEDOT:PSS gold standard. Furthermore, PEDOT:CTPR3 dispersion is successfully optimized for inkjet printing, preserving its electroactivity properties after printing. This approach opens the door to the use of these novel hybrids for bioelectronics.

Engineering bio-brick protein scaffolds for organizing enzyme assemblies

Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi-enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6-fold compared to free enzymes, with the covalent stapling outperforming the metal-driven assembly. This enhancement likely stems from higher-order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial-organizing tools, for more efficient enzymatic cascade reactions.

The roles of templates consisting of amino acids in the synthesis and application of gold nanoclusters

Gold nanoclusters (AuNCs) with low toxicity, high photostability, and facile synthesis have attracted great attention. The ligand is of great significance in stabilizing AuNCs and regulating their properties. Ligands consisting of amino acids (proteins and peptides) are an ideal template for synthesizing applicative AuNCs due to their inherent bioactivity, biocompatibility, and accessibility. In this review, we summarize the correlation of the template consisting of amino acids with the properties of AuNCs by analyzing different peptide sequences. The selection of amino acids can regulate the fluorescence excitation/emission and intensity, size, cell uptake, and light absorption. By analyzing the role played by AuNCs stabilized by proteins and peptides in the application, universal rules and detailed performances of sensors, antibacterial agents, therapeutic reagents, and light absorbers are reviewed. This review can guide the template design and application of AuNCs when selecting proteins and peptides as ligands.

Design of a gold nanoparticles site in an engineered lipase: an artificial metalloenzyme with enantioselective reductase-like activity

The conjugation of gold complexes with proteins has proved to be interesting and effective in obtaining artificial metalloenzymes as catalysts with improved properties such as higher stability, activity and selectivity. However, the design and precise regulation of their structure as protein nanostructured forms level remains a challenge. Here, we have designed and constructed a gold nanoparticles-enzyme bioconjugate, by tailoring the in situ formation of gold nanoparticles (AuNPs) at two specific sites on the structure of an alkalophilic lipase from Geobacillus thermocatenulatus (GTL). For this purpose, two genetically modified variants of GTL were created by inserting a unique cysteine residue into the catalytic active site by replacing the active serine (GTL-114) and into the lid site (GTL-193). The enzyme, after a first protein-gold coordination, induced the in situ formation of AuNPs, generating a homogeneous artificial enzyme. The size and morphology of the nanoparticles in the AuNPs-enzyme conjugate have been controlled by specific pH conditions in synthesis and the specific protein region where they are formed. Reductase activity of all of them was confirmed in the hydrogenation of nitroarenes in aqueous media. The protein area seemed to be key for the AuNPs, with the best TOF values obtained for the bioconjugates with AuNPs in the lid site. Finally, the protein environment and the asymmetric properties of the AuNPs were tested in the reduction of acetophenone to 1-phenylethanol in aqueous medium at room temperature. A high reductive conversion and an enantiomeric excess of up to 39% towards (R)-1-phenylethanol was found using Au-Mt@GTL-114 pH 10 as a catalyst. Moderate enantioselectivity towards the opposite isomer was also observed using the Au-Mt@GTL-193 pH 10 conjugate.

Photoluminescent Characterization of Metal Nanoclusters: Basic Parameters, Methods, and Applications

Metal nanoclusters (MNCs) can be synthesized with atomically precise structures and molecule formulae due to the rapid development of nanocluster science in recent decades. The ultrasmall size range (normally < 2 nm) endows MNCs with plenty of molecular-like properties, among which photoluminescent properties have aroused extensive attention. Tracing the research and development processes of luminescent nanoclusters, various photoluminescent analysis and characterization methods play a significant role in elucidating luminescent mechanism and analyzing luminescent properties. In this review, it is aimed to systematically summarize the normally used photoluminescent characterizations in MNCs including basic parameters and methods, such as excitation/emission wavelength, quantum yield, and lifetime. For each key parameter, first its definition and meaning is introduced and then the relevant characterization methods including measuring principles and the revelation of luminescent properties from the collected data are discussed. Then, it is discussed in details how to explore the luminescent mechanism of MNCs and construct NC-based applications based on the measured data. By means of these characterization strategies, the luminescent properties of MNCs and NC-based designs can be explained quantitatively and qualitatively. Hence, this review is expected to provide clear guidance for researchers to characterize luminescent MNCs and better understand the luminescent mechanism from the measured results.

In vitro Production of Hemin-Based Artificial Metalloenzymes

Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.

Size and charge effects of metal nanoclusters on antibacterial mechanisms

Nanomaterials, specifically metal nanoclusters (NCs), are gaining attention as a promising class of antibacterial agents. Metal NCs exhibit antibacterial properties due to their ultrasmall size, extensive surface area, and well-controlled surface ligands. The antibacterial mechanisms of metal NCs are influenced by two primary factors: size and surface charge. In this review, we summarize the impacts of size and surface charge of metal NCs on the antibacterial mechanisms, their interactions with bacteria, and the factors that influence their antibacterial effects against both gram-negative and gram-positive bacteria. Additionally, we highlight the mechanisms that occur when NCs are negatively or positively charged, and provide examples of their applications as antibacterial agents. A better understanding of relationships between antibacterial activity and the properties of metal NCs will aid in the design and synthesis of nanomaterials for the development of effective antibacterial agents against bacterial infections. Based on the remarkable achievements in the design of metal NCs, this review also presents conclusions on current challenges and future perspectives of metal NCs for both fundamental investigations and practical antibacterial applications.

Nanozymes with versatile redox capabilities inspired in metalloenzymes

Metalloenzymes represent exemplary systems in which an organic scaffold combines with a functional inorganic entity, resulting in excellent redox catalysts. Inspired by these natural hybrid biomolecules, biomolecular templates have garnered significant attention for the controlled synthesis of inorganic nanostructures. These nanostructures ultimately benefit from the protection and colloidal stabilization provided by the biomacromolecule. In this study, we have employed this strategy to prepare nanozymes with redox capabilities, utilizing the versatile catalytic profile of Pt-loaded nanomaterials. Thus, we have investigated protein-templated Pt-based nanoclusters of different sizes and compositions, which exhibit remarkable oxidase, catalase, and reductase-like activities. The interplay between the composition and catalytic activity highlighted the size of the nanocluster as the most prominent factor in determining the performance of the nanozymes. Additionally, we have demonstrated the use of protein-templated nanozymes as potential co-catalysts in combination with enzymes for coupled reactions, under both sequential and concurrent one-pot conditions. This study provides valuable insights into nanozyme design and its wide range of applications in the design of complex catalytic systems.

Synthesis of Greenish-Yellow Fluorescent Copper Nanocluster for the Selective and Sensitive Detection of Fipronil Pesticide in Vegetables and Grain Samples

In this paper, a new synthetic route is introduced for the synthesis of high-luminescent greenish-yellow fluorescent copper nanoclusters (PVP@A. senna-Cu NCs) using Avaram senna (A. senna) and polyvinylpyrrolidone (PVP) as templates. A. senna plant extract mainly contains variety of phytochemicals including glycosides, sugars, saponins, phenols, and terpenoids that show good pharmacological activities such as anti-inflammatory, antioxidant, and antidiabetic. PVP is a stable and biocompatible polymer that is used as a stabilizing agent for the synthesis of PVP@A. senna-Cu NCs. The size, surface functionality, and element composition of the fabricated Cu NCs were confirmed by various analytical techniques. The as-prepared greenish-yellow fluorescent Cu NCs exhibit significant selectivity towards fipronil, thereby favoring to assay fipronil pesticide with good linearity in the range of 3.0-30 μM with a detection limit of 65.19 nM. More importantly, PVP@A. senna-Cu NCs are successfully applied to assay fipronil in vegetable and grain samples.

Potential impact of various surface ligands on the cellular uptake and biodistribution characteristics of red, green, and blue emitting Cu nanoclusters

Surface functionalization has a prominent influence on tuning/manipulating the physicochemical properties of nanometer scaled materials. Ultrasmall sized nanoclusters with very few atoms have received enormous attention due to their bright fluorescence, biocompatibility, lower toxicity, good colloidal stability and strong photostability. These properties make them suitable for diagnostic applications. In this work, we intend to study the effect of surface functional ligands on their biodistribution both in vitro and in vivo organelle systems for bioimaging applications.

Protein-Templated Metal Nanoclusters: Molecular-like Hybrids for Biosensing, Diagnostics and Pharmaceutics

The use of proteins as biomolecular templates to synthesize atomically precise metal nanoclusters has been gaining traction due to their appealing properties such as photoluminescence, good colloidal- and photostability and biocompatibility. The synergistic effect of using a protein scaffold and metal nanoclusters makes it especially attractive for biomedical applications. Unlike other reviews, we focus on proteins in general as the protective ligand for various metal nanoclusters and highlight their applications in the biomedical field. We first introduce the approaches and underlined principles in synthesizing protein-templated metal nanoclusters and summarize some of the typical proteins that have been used thus far. Afterwards, we highlight the key physicochemical properties and the characterization techniques commonly used for the size, structure and optical properties of protein-templated metal nanoclusters. We feature two case studies to illustrate the importance of combining these characterization techniques to elucidate the formation process of protein-templated metal nanoclusters. Lastly, we highlight the promising applications of protein-templated metal nanoclusters in three areas-biosensing, diagnostics and therapeutics.

Luminescent Gold Nanoclusters for Bioimaging: Increasing the Ligand Complexity

Fluorescence, and more in general, photoluminescence (PL), presents important advantages for imaging with respect to other diagnostic techniques. In particular, detection methodologies exploiting fluorescence imaging are fast and versatile; make use of low-cost and simple instrumentations; and are taking advantage of newly developed powerful, low-cost, light-based electronic devices, such as light sources and cameras, used in huge market applications, such as civil illumination, computers, and cellular phones. Besides the aforementioned simplicity, fluorescence imaging offers a spatial and temporal resolution that can hardly be achieved with alternative methods. However, the two main limitations of fluorescence imaging for bio-application are still (i) the biological tissue transparency and autofluorescence and (ii) the biocompatibility of the contrast agents. Luminescent gold nanoclusters (AuNCs), if properly designed, combine high biocompatibility with PL in the near-infrared region (NIR), where the biological tissues exhibit higher transparency and negligible autofluorescence. However, the stabilization of these AuNCs requires the use of specific ligands that also affect their PL properties. The nature of the ligand plays a fundamental role in the development and sequential application of PL AuNCs as probes for bioimaging. Considering the importance of this, in this review, the most relevant and recent papers on AuNCs-based bioimaging are presented and discussed highlighting the different functionalities achieved by increasing the complexity of the ligand structure.

Engineered Protein-Driven Synthesis of Tunable Iron Oxide Nanoparticles as T1 and T2 Magnetic Resonance Imaging Contrast Agents

Iron oxide nanoparticles (IONPs) have become one of the most promising nanomaterials for biomedical applications because of their biocompatibility and physicochemical properties. This study demonstrates the use of protein engineering as a novel approach to design scaffolds for the tunable synthesis of ultrasmall IONPs. Rationally designed proteins, containing different number of metal-coordination sites, were evaluated to control the size and the physicochemical and magnetic properties of a set of protein-stabilized IONPs (Prot-IONPs). Prot-IONPs, synthesized through an optimized coprecipitation approach, presented good T1 and T2 relaxivity values, stability, and biocompatibility, showing potential for magnetic resonance imaging (MRI) applications.

Microwave-Assisted Synthesis of Red Emitting Copper Nanoclusters Using Trypsin as a Ligand for Sensing of Pb2+ And Hg2+ Ions in Water and Tobacco Samples

In this work, a microwave assisted method was developed for synthesis of red fluorescent copper nanoclusters (NCs) using trypsin as a template (trypsin-Cu). The as-synthesized trypsin-Cu NCs are stable and water soluble, exhibiting fluorescence emission at 657 nm when excited at 490 nm. The as-prepared red-emitting trypsin-Cu NCs were characterized by using several analytical techniques such as ultraviolet-visible (UV-Vis) and fluorescence, fluorescence lifetime, Fourier transform infrared, and X-ray photoelectron spectroscopic techniques. Red-emitting trypsin-Cu NCs acted as a nanosensor for sensing both Pb2+ and Hg2+ ions through fluorescence quenching. Using this approach, good linearities are observed in the range of 0.1-25 and of 0.001-1 μM with the lower limit of detection of 14.63 and 56.81 nM for Pb2+ and Hg2+ ions, respectively. Trypsin-Cu NCs-based fluorescence assay was successfully applied to detect both Hg2+ and Pb2+ ions in water and tobacco samples.

MIB2: metal ion-binding site prediction and modeling server

MOTIVATION

MIB2 (metal ion-binding) attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types.

RESULTS

MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more MIB residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions.

AVAILABILITY AND IMPLEMENTATION

Freely available on the web at http://bioinfo.cmu.edu.tw/MIB2/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Mercury mediated DNA-Au/Ag nanocluster ensembles to generate a gray code encoder for biocomputing

Boolean operations utilizing DNA as a platform for biocomputing have become a promising tool for next-generation bio-molecular computers. In the whole process of any binary data transmission, bit errors are unavoidable and commonly occur. Cascades of exclusive-OR (XOR) operations show the great potential to evaluate these errors by introducing a parity generator (pG) and a parity checker (pC). Herein, we constructed a DNA hybrid architecture platform employing a chemosensing ensemble of mercury-mediated DNA-Au/Ag nanoclusters (M-Au/Ag NCs) to operate unconventional pG/pC for "error detection". Taking advantage of pG/pC, the transmitted and received data is converted to secure information using a binary to gray code encoder. To the best of our knowledge, this is the first molecular gray code encoder for biocomputing, which discovers an exciting avenue to protect information security through sophisticated logic circuits.

Fabrication of avidin-stabilized gold nanoclusters with dual emissions and their application in biosensing

Protein-stabilized gold nanoclusters (Prot-Au NCs) have been widely used in biosensing and cell imaging owing to their excellent optical properties and low biotoxicity. However, several Prot-Au NCs reported in the literature do not retain the biological role of the protein, which greatly limits their ability to directly detect biomarkers. This study demonstrated for the first time the successful synthesis of dual-function avidin-stabilized gold nanoclusters (Av–Au NCs) using a one-pot method. The resulting Av–Au NCs exhibited intense blue and red emissions under 374 nm excitation. Furthermore, the Av–Au NCs retained the native functionality of avidin to bind to biotin. When DNA strands modified with biotin at both ends (i.e., linker chains) were mixed with Av–Au NCs, large polymers were formed, indicating that Av–Au NCs could achieve fluorescence signal amplification by interacting with biotin. Taking advantage of the aforementioned properties, we constructed a novel enzyme-free fluorescent biosensor based on the Av–Au NCs-biotin system to detect DNA. The designed fluorescent biosensor could detect target DNA down to 0.043 nM, with a wide line range from 0.2 nM to 20 µM. Thus, these dual-functional Av–Au NCs were shown to be an excellent fluorescent material for biosensing.

Avidin-stabilized gold nanoclusters (Av–Au NCs) were synthesized for the first time by a water-bath method.

The synthesized Av–Au NCs not only exhibited intense blue and red emissions under 374 nm excitation, but also retained the native functionality of avidin to bind to biotin.

The fluorescent signal amplification system constructed by the interaction of Av–Au NCs with biotin was successfully applied to detect target DNA in vitro.

Photoluminescent nanocluster-based probes for bioimaging applications

In the continuous search for versatile and better performing probes for optical bioimaging and biosensing applications, many research efforts have focused on the design and optimization of photoluminescent metal nanoclusters. They consist of a metal core composed by a small number of atoms (diameter < 2-3 nm), usually coated by a shell of stabilizing ligands of different nature, and are characterized by molecule-like quantization of electronic states, resulting in discrete and tunable optical transitions in the UV-Vis and NIR spectral regions. Recent advances in their size-selective synthesis and tailored surface functionalization have allowed the effective combination of nanoclusters and biologically relevant molecules into hybrid platforms, that hold a large potential for bioimaging purposes, as well as for the detection and tracking of specific markers of biological processes or diseases. Here, we will present an overview of the latest combined imaging or sensing nanocluster-based systems reported in the literature, classified according to the different families of coating ligands (namely, peptides, proteins, nucleic acids, and biocompatible polymers), highlighting for each of them the possible applications in the biomedical field.

A visualized ratiometric fluorescence sensing system for copper ions based on gold nanoclusters/perovskite quantum dot@SiO2 nanocomposites

Excessive copper ions (Cu²⁺) cause serious environmental pollution and even endanger the health of organisms. Fluorescence chemosensing materials are widely used in the detection of metal ions due to their simple operation and high sensitivity. In this study, SiO₂-encapsulated single perovskite quantum dot (PQD@SiO₂) core-shell nanostructures which show strong, stable, and green fluorescence are synthesized and composited with gold nanoclusters (AuNCs) which show Cu²⁺-sensitive and red light-emitting fluorescence to obtain a visualized ratiometric fluorescence sensor (AuNCs/PQD@SiO₂) for the detection of Cu²⁺. In the visualized detection of Cu²⁺, the green fluorescence emitted from the ion-insensitive PQD@SiO₂ component is used as a reference signal and the red fluorescence emitted by ion-sensitive AuNC component is adopted as a sensing signal. In the presence of Cu²⁺, the red fluorescence is quenched whereas the green fluorescence remains stable, which results in a visualized fluorescence color change from orange-red to yellow and finally to green with increasing Cu²⁺ concentration. The significant change in the fluorescence color of AuNCs/PQD@SiO₂ in response to Cu²⁺ enables a rapid, sensitive, and visualized detection of Cu²⁺. Further accurate and sensitive ratiometric fluorescence analysis of Cu²⁺ can be accomplished by measuring the ratio of fluorescence intensities at 643 and 520 nm (I₆₄₃/I₅₂₀) at a certain Cu²⁺ level. The developed AuNCs/PQD@SiO₂-based sensor has been validated by its satisfactory application in the detection of Cu²⁺ in human serum and environmental water samples.

Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids

Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein–nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine.

A novel 3D cryo correlative approach locates designed therapeutic protein–nanomaterial hybrids in whole cells with high specificity and resolution. Detection of treatment-induced morphological changes, crucial for pre-clinical studies, are revealed.

Boosting the Photoluminescent Properties of Protein-Stabilized Gold Nanoclusters through Protein Engineering

This work reports on the use of protein engineering as a versatile tool to rationally design metal-binding proteins for the synthesis of highly photoluminescent protein-stabilized gold nanoclusters (Prot-AuNCs). The use of a single repeat protein scaffold allowed the incorporation of a set of designed metal-binding sites to understand the effect of the metal-coordinating residues and the protein environment on the photoluminescent (PL) properties of gold nanoclusters (AuNCs). The resulting Prot-AuNCs, synthesized by two sustainable procedures, showed size-tunable color emission and outstanding PL properties. In a second stage, tryptophan (Trp) residues were introduced at specific positions to provide an electron-rich protein environment and favor energy transfer from Trps to AuNCs. This modification resulted in improved PL properties relevant for future applications in sensing, biological labeling, catalysis, and optics.

Engineered Repeat Protein Hybrids: The New Horizon for Biologic Medicines and Diagnostic Tools

ConspectusThe last decades have witnessed unprecedented scientific breakthroughs in all the fields of knowledge, from basic sciences to translational research, resulting in the drastic improvement of the lifespan and overall quality of life. However, despite these great advances, the treatment and diagnosis of some diseases remain a challenge. Inspired by nature, scientists have been exploring biomolecules and their derivatives as novel therapeutic/diagnostic agents. Among biomolecules, proteins raise much interest due to their high versatility, biocompatibility, and biodegradability.Protein binders (binders) are proteins that bind other proteins, in certain cases, inhibiting or modulating their action. Given their therapeutic potential, binders are emerging as the next generation of biopharmaceuticals. The most well-known example of binders are antibodies, and inspired by them researchers have developed alternative binders using protein design approaches. Protein design can be based on naturally occurring proteins in which, by means of rational design or combinatorial approaches, new binding interfaces can be engineered to obtain specific functions or based on de novo proteins emerging from state-of-the-art computational methodologies.Among the novel designed proteins, a class of engineered repeat proteins, the consensus tetratricopeptide repeat (CTPR) proteins, stand out due to their stability and robustness. The CTPR unit is a helix-turn-helix motif constituted of 34 amino acids, of which only 8 are essential to ensure correct folding of the structure. The small number of conserved residues of CTPR proteins leaves plenty of freedom for functional mutations, making them a base scaffold that can be easily and reproducibly tailored to endow desired functions to the protein. For example, the introduction of metal-binding residues (e.g., histidines, cysteines) drives the coordination of metal ions and the subsequent formation of nanomaterials. Additionally, the CTPR unit can be conjugated with other peptides/proteins or repeated in tandem to encode larger CTPR proteins with superhelical structures. These properties allow for the design of both binder and nanomaterial-coordination modules as well as their combination within the same molecule, making the CTPR proteins, as we have demonstrated in several recent examples, the ideal platform to develop protein-nanomaterial hybrids. Generally, the fusion of two distinct materials exploits the best properties of each; however, in protein-nanomaterial hybrids, the fusion takes on a new dimension as new properties arise.These hybrids have ushered the use of protein-based nanomaterials as biopharmaceuticals beyond their original therapeutic scope and paved the way for their use as theranostic agents. Despite several reports of protein-stabilized nanomaterials found in the literature, these systems offer limited control in the synthesis and properties of the grown nanomaterials, as the protein acts just as a stabilizing agent with no significant functional contribution. Therefore, the rational design of protein-based nanomaterials as true theranostic agents is still incipient. In this context, CTPR proteins have emerged as promising scaffolds to hold simultaneously therapeutic and diagnostic functions through protein engineering, as it has been recently demonstrated in pioneering in vitro and in vivo examples.

Development of a Hybrid Bioinorganic Nanobiocatalyst: Remarkable Impact of the Immobilization Conditions on Activity and Stability of β-Galactosidase

Hybrid bioinorganic biocatalysts have received much attention due to their simple synthesis, high efficiency, and structural features that favor enzyme activity and stability. The present work introduces a biomineralization strategy for the formation of hybrid nanocrystals from β-galactosidase. The effects of the immobilization conditions were studied, identifying the important effect of metal ions and pH on the immobilization yield and the recovered activity. For a deeper understanding of the biomineralization process, an in silico study was carried out to identify the ion binding sites at the different conditions. The selected β-galactosidase nanocrystals showed high specific activity (35,000 IU/g biocatalyst) and remarkable thermal stability with a half-life 11 times higher than the soluble enzyme. The nanobiocatalyst was successfully tested for the synthesis of galacto-oligosaccharides, achieving an outstanding performance, showing no signs of diffusional limitations. Thus, a new, simple, biocompatible and inexpensive nanobiocatalyst was produced with high enzyme recovery (82%), exhibiting high specific activity and high stability, with promising industrial applications.

Rapid synthesis of fluorescent bovine serum albumin-gold nanoclusters complex for glutathione determination

A facile one-pot method for synthesis of bovine serum albumin (BSA)-gold nanoclusters (AuNCs) has been developed. The formation of BSA-AuNCs took only 30 s under mild conditions. BSA-AuNCs exhibited strong orange-yellow fluorescence, and the excitation and emission peaks were at 370 nm and 564 nm, respectively. In the process of forming BSA-AuNCs, the molecular chain of BSA has not been destroyed. Moreover, there were a large number of Au cations on the surface of BSA-AuNCs, which had strong oxidizing abilities. The reason for the ultrabright fluorescence of BSA-AuNCs was attributed to the Au(0)@Au(I)@Au(III)-ligand structure on the surface of BSA. In order to evaluate the fluorescence performance of BSA-AuNCs, BSA-AuNCs was used as a probe, realizing the sensitive and selective determination of glutathione (GSH) in a wide linear range of 0.01-0.48 μM and a detection limit of 3.3 nM. The proposed method not only offers a brand-new scheme for synthesizing BSA-AuNCs, but also provides a platform for studying the interaction between metal core and proteins. A facile one-pot method to synthesize ultrabright fluorescent BSA-AuNCs in tens of seconds has been introduced by mixing BSA suspension, KSCN, and HAuCl₄. The as-prepared BSA-AuNCs showed intensive orange-yellow fluorescence under a UV lamp (365 nm)_, and BSA still keeps the integral molecular chains during the whole synthesis process. Moreover, the as-prepared BSA-AuNCs have realized the sensitive and selective detection of glutathione (GSH) in a wide linear range of 0.01-0.48 μM and a detection limit of 3.3 nM.

Nanotheranostic Application of Fluorescent Protein-Gold Nanocluster Hybrid Materials: A Mini-review

The gold nanoclusters (Au NCs) are a special kind of gold nanomaterial containing several gold atoms. Because of their small size and large surface area, Au NCs possess macroscopic quantum tunneling and dielectric domain effects. Furthermore, Au NCs fluorescent materials have longer luminous time and better photobleaching resistance compared with other fluorescent materials. The synthetic process of traditional Au NCs is complicated. Traditional Au NCs are prepared mainly by using polyamide amine type dendrites, and sixteen alkyl trimethylamine bromide or sulfhydryl small molecule as stabilizers. They are consequently synthesized by the reduction of strong reducing agents such as sodium borohydride. Notably, these materials are toxic and environmental-unfriendly. Therefore, there is an urgent need to develop more effective methods for synthesizing Au NCs via a green approach. On the other hand, the self-assembly of protein gold cluster-based materials, and their biomedical applications have become research hotspots in this field. We have been working on the synthesis, assembly and application of protein conjugated gold clusters for a long time. In this review, the synthesis and assembly of protein-gold nanoclusters and their usage in cell imaging and other medical research are discussed.

Synergistic integration of metal nanoclusters and biomolecules as hybrid systems for therapeutic applications

Therapeutic nanoparticles are designed to enhance efficacy, real-time monitoring, targeting accuracy, biocompatibility, biodegradability, safety, and the synergy of diagnosis and treatment of diseases by leveraging the unique physicochemical and biological properties of well-developed bio-nanomaterials. Recently, bio-inspired metal nanoclusters (NCs) consisting of several to roughly dozens of atoms (<2 nm) have attracted increasing research interest, owing to their ultrafine size, tunable fluorescent capability, good biocompatibility, variable metallic composition, and extensive surface bio-functionalization. Hybrid core-shell nanostructures that effectively incorporate unique fluorescent inorganic moieties with various biomolecules, such as proteins (enzymes, antigens, and antibodies), DNA, and specific cells, create fluorescently visualized molecular nanoparticle. The resultant nanoparticles possess combinatorial properties and synergistic efficacy, such as simplicity, active bio-responsiveness, improved applicability, and low cost, for combination therapy, such as accurate targeting, bioimaging, and enhanced therapeutic and biocatalytic effects. In contrast to larger nanoparticles, bio-inspired metal NCs allow rapid renal clearance and better pharmacokinetics in biological systems. Notably, advances in nanoscience, interfacial chemistry, and biotechnologies have further spurred researchers to explore bio-inspired metal NCs for therapeutic purposes. The current review presents a comprehensive and timely overview of various metal NCs for various therapeutic applications, with a special emphasis on the design rationale behind the use of biomolecules/cells as the main scaffolds. In the different hybrid platform, we summarize the current challenges and emerging perspectives, which are expected to offer in-depth insight into the rational design of bio-inspired metal NCs for personalized treatment and clinical translation.

Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics

As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.

Repeat proteins: designing new shapes and functions for solenoid folds

The modular nature of repeat proteins has inspired the design of regular and completely novel sequences and structures. Research in the past years has provided a broad set of design approaches and new repeat proteins that have found applications in molecular recognition, taking advantage of the natural ability of some of these families to bind proteins, peptides and nucleic acids. Here, we provide an overview on the recent trends in design of repeat proteins, particularly solenoid folds, and their applications. By exploiting the intrinsic modularity of repeats, new architectures have been designed that combine different types of repeat, are easily scalable by changing the number of repeats and can be quickly generated by using existing modular building blocks.

Biomarker sensing platforms based on fluorescent metal nanoclusters

Metal nanoclusters (NCs) and their unique properties are increasing in importance and their applications are covering a wide range of areas. Their remarkable fluorescence properties and easy synthesis procedure and the possibility of functionalizing them for the detection of specific targets, such as biomarkers, make them a very interesting biosensing tool. Nowadays the detection of biomarkers related to different diseases is critical. In this context, NCs scaffolded within an appropriate molecule can be used to detect and quantify biomarkers through specific interactions and fluorescence properties of the NCs. These methods include analytical detection and biolocalization using imaging techniques. This review covers a selection of recent strategies to detect biomarkers related to diverse diseases (from infectious, inflammatory, or tumour origin) using fluorescent nanoclusters.

Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis

Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.

An Adhesive Peptide from the C-Terminal Domain of α-Synuclein for Single-Layer Adsorption of Nanoparticles onto Substrates

The two-dimensional (2D) homogeneous assembly of nanoparticle monolayer arrays onto a broad range of substrates constitutes an important challenge for chemistry, nanotechnology, and material science. α-Synuclein (αS) is an intrinsically disordered protein associated with neuronal protein complexes and has a high degree of structural plasticity and chaperone activity. The C-terminal domain of αS has been linked to the noncovalent interactions of this protein with biological targets and the activity of αS in presynaptic connections. Herein, we have systematically studied peptide fragments of the chaperone-active C-terminal sequence of αS and identified a 17-residue peptide that preserves the versatile binding nature of αS. Attachment of this short peptide to gold nanoparticles afforded colloidally stable nanoparticle suspensions that allowed the homogeneous 2D adhesion of the conjugates onto a wide variety of surfaces, including the formation of crystalline nanoparticle superlattices. The peptide sequence and the strategy reported here describe a new adhesive molecule for the controlled monolayer adhesion of metal nanoparticles and sets a stepping-stone toward the potential application of the adhesive properties of αS.

Engineering multifunctional metal/protein hybrid nanomaterials as tools for therapeutic intervention and high-sensitivity detection

Protein-based hybrid nanomaterials have recently emerged as promising platforms to fabricate tailored multifunctional biologics for biotechnological and biomedical applications. This work shows a simple, modular, and versatile strategy to design custom protein hybrid nanomaterials. This approach combines for the first time the engineering of a therapeutic protein module with the engineering of a nanomaterial-stabilizing module within the same molecule, resulting in a multifunctional hybrid nanocomposite unachievable through conventional material synthesis methodologies. As the first proof of concept, a multifunctional system was designed ad hoc for the therapeutic intervention and monitoring of myocardial fibrosis. This hybrid nanomaterial combines a designed Hsp90 inhibitory domain and a metal nanocluster stabilizing module resulting in a biologic drug labelled with a metal nanocluster. The engineered nanomaterial actively reduced myocardial fibrosis and heart hypertrophy in an animal model of cardiac remodeling. In addition to the therapeutic effect, the metal nanocluster allowed for in vitro, ex vivo, and in vivo detection and imaging of the fibrotic disease under study. This study evidences the potential of combining protein engineering and protein-directed nanomaterial engineering approaches to design custom nanomaterials as theranostic tools, opening up unexplored routes to date for the next generation of advanced nanomaterials in medicine.

Engineering protein-based hybrids by combining protein engineering and nanotechnology: a protein-nanocluster hybrid for theranostic use in myocardial fibrosis shows the potential to create tailored multifunctional biologics for biomedicine.

Rapid conversion from common precursors to carbon dots in large scale: Spectral controls, optical sensing, cellular imaging and LEDs application

The commercial production of carbon dots will be concerned with the simplicity and energy consumption. Herein, maleic acid and m-phenylenediamine form elegantly simple sources for carbon dots. The two precursors are dissolved in formamid (abbreviated as FA) or N,N-dimethylformamide (abbreviated as DMF) and the dehydration-condensation processes have been performed at 30 min or 120 min under room temperature. No external energy/irradiations, reactants or high temperature will be required and the afforded carbon dots (abbreviated as CDs) are collected by extraction, centrifugation, dialysis and column chromatography. It has been found for the first time the choice of organic solvents has been correlated with emission color. The blue-emitting CDs (abbreviated as B-CDs) and green-emitting CDs (abbreviated as G-CDs) are yielded in FA and DMF respectively. Facts support that the increase of -CONH- units causes red-shift in emissions. The optical sensing of tetracycline has been explored and the detection limit of blue-emitting CDs is as low as 25 nM. Live cells exposed to B-CDs and G-CDs (0.5 mg/ml) show no apparent changes via both Cell Counting Kit-8 and Annexin V/7-AAD analysis. The blue and green fluorescent signals can be easily tracked in cells. It has been demonstrated that the two carbon dots can be fabricated as multiple-color light-emitting diodes (abbreviated as LEDs).

Antibody-Directed Synthesis of Catalytic Nanoclusters for Bioanalytical Assays

Synthesis of atomic nanoclusters (NCs) using proteins as a scaffold has attracted great attention. Usually, the synthetic conditions for the synthesis of NCs stabilized with proteins require extreme pH values or temperature. These harsh reaction conditions cause the denaturation of the proteins and end up in the loss of their biological functions. Until now, there are no examples of the use of antibodies as NC stabilizers. In this work, we present the first method for the synthesis of catalytic NCs that uses antibodies for the stabilization of NCs. Anti-BSA IgG was used as a model to demonstrate that it is possible to use an antibody as a scaffold for the synthesis of semiconductor and metallic NCs with catalytic properties. The synthesis of antibodies modified with NCs is carried out under nondenaturing conditions, which do not affect the antibody structure. The resulting antibodies still maintain the affinity for target antigens and protein G. The catalytic properties of the anti-BSA IgG modified with NCs can be used to the quantification of bovine serum albumin (BSA) in a direct sandwich enzyme-linked immunosorbent assay (ELISA).

Peptide and protein modified metal clusters for cancer diagnostics

The biomedical features of metal clusters have been explored in tumor diagnostic applications in recent years. Peptide or protein protected metal clusters with low toxicity, ultra-small size and good biocompatibility are ideal bioanalytical tools, and exhibit better cancer diagnostic properties that have been attractive to oncologists. This perspective provides a rigorous but succinct overview of cancer diagnosis as a working concept for metal clusters by reporting the latest significant advances in the applications of metal clusters in tumor-related bioanalysis and diagnosis. The materials design principles, bioanalytical mechanisms and biomedical applications of metal clusters are described, and then the potential challenges and prospects of metal clusters in cancer diagnosis are discussed. A perspective addressing the role of metal clusters in this field is required to understand their effects and functions, as well as for the scientific community to further advance the development of metal clusters for broader diagnostic applications.

Protein-based functional hybrid bionanomaterials by bottom-up approaches

This review aims to summarize the last advances on the field of protein engineering towards functional bionanomaterials. Albeit being this an emerging research field, multidisciplinary perspectives in the design of synthetic protein-based hybrid bionanomaterials have resulted in significant progresses. The review covers the definition of bionanomaterials as such and the description of the main methodological approaches currently employed for their assembly. In this context, special emphasis is placed on the fundamental role of protein design. Then, a general overview of the most recent advances related to the fabrication and application of protein-based bionanomaterials in several applications is provided, with special focus on catalysis. Finally, key aspects to be considered by the research community to establish the path for significant future developments in this promising field are discussed.

Photonic crystal enhanced gold-silver nanoclusters fluorescent sensor for Hg2+ ion

Luminescent nanoclusters (NCs) have attracted much attention because of their good photostability and low toxicity, however, the low quantum yield is still a deficiency, and many increasing efforts are being devoted to enhance the luminescence intensity of NCs. In this paper, a method of enhancing the fluorescent signal of gold-silver nanoclusters (AuAgNCs) by photonic crystals (PhCs) was proposed. The fluorescent intensity of AuAgNCs on PhCs can be enhanced 8.0-fold in comparison to the control sample without PhCs. Furthermore, a novel fluorescence sensor of AuAgNCs based on PhCs is used for the sensitive and selective detection of Hg²⁺ ion in the aqueous solution, the detection limit is 0.35 nM due to the PhCs enhancement effect for the fluorescence. This proposed method may not only develop a highly sensitive method for determination of Hg²⁺ ion, but also expand the application of AuAgNCs in ultra-trace analysis.

White-emitting Protein-Metal Nanocluster Phosphors for Highly Performing Biohybrid Light-Emitting Diodes

This work presents a simple in situ synthesis and stabilization of fluorescent gold nanoclusters (AuNCs) with different sizes using engineered protein scaffolds in water. The protein-AuNC hybrids show a dual emission (450 and 700 nm) with a record photoluminescence quantum yield of 20%. These features impelled us to apply them to biohybrid light-emitting diodes as color down-converting filters or biophosphors. Efficient white emission (x/y CIE color coordinates of 0.31/0.29) and stabilities of more than 800 h were achieved. This represents a 2 orders of magnitude enhancement compared to the prior art. Besides the outstanding performance, the protein scaffold also infers a unique anisotropic emission character that is considered as a proof-of-concept of high interest for single-point lighting and display.

Protein-directed crystalline 2D fullerene assemblies

Water soluble 2D crystalline monolayers of fullerenes grow on planar assemblies of engineered consensus tetratricopeptide repeat proteins. Designed fullerene-coordinating tyrosine clamps on the protein introduce specific fullerene binding sites, which facilitate fullerene nucleation. Through reciprocal interactions between the components, the hybrid material assembles into two-dimensional 2 nm thick structures with crystalline order, that conduct photo-generated charges. Thus, the protein-fullerene hybrid material is a demonstration of the developments toward functional materials with protein-based precision control of functional elements.

Palladium Nanoclusters Confined in MOF@COP as a Novel Nanoreactor for Catalytic Hydrogenation

Metal-nanocluster-doped porous materials are attracting considerable research attention due to their specific catalytic performance. In this study, core-shell metal-organic frameworks@covalent organic polymer (MOF@COP) nanocomposites were formed by the covalent linking of chemically stable COP on the surface of size-selective UiO-66-NH₂. Pd nanoclusters with an average diameter of ∼0.8 nm were successfully confined in UiO-66-NH₂@COP, and the obtained nanoreactor, referred to as UiO-66-NH₂@COP@Pd, exhibited abundant porosity, high stability, and large surface area. Notably, the UiO-66-NH₂@COP@Pd nanoreactor exhibited superior catalytic activity and stability for the catalytic reduction of 4-nitrophenol and hydrogenation of other nitroarenes, demonstrating the potential of Pd-cluster-doped MOF@COP hybrid materials as candidates for efficient catalytic hydrogenation. This study may provide new avenues for the construction of MOF@COP-hybrid-material-based heterogeneous catalysts for efficient catalytic applications.

Purification and separation of ultra-small metal nanoclusters

Metal nanoclusters (NCs) are ultra-small nanoparticles intermediate in size between small molecule complexes and nanoparticles. NCs with tunable surface functionality feature unique physical and chemical properties, however these properties are frequently compromised by the presence of undesired components such as excess ligands or mixtures of NCs. In a typical synthesis process, different NCs can be formed with varying numbers of metal atoms and/or ligands, and even NCs with the same number of metal atoms and ligands can have different spatial structures. The separation of pure NCs is important because different species have distinct optical and catalytic behavior. However, NCs can be difficult to purify or separate for a range of reasons. In this review, we discuss established and emerging approaches for NC purification/separation, with a focus on choosing the appropriate method depending on NC and application.

Red fluorescent AuNDs with conjugation of cholera toxin subunit B (CTB) for extended-distance retro-nerve transporting and long-time neural tracing

A retrograde transportation nerve probe, Au nanodots-cholera toxin B subunit (AuNDs-CTB), are prepared and fully characterized, which emit bright red fluorescence and show high quantum yield (7.2%) and good stability. The fluorescence emitted by the AuNDs is constant across a wide pH range (4-10) and after prolonged UV irradiation (>4 h). Previously, CTB has shown targeting characteristic for nerve cells with high sensitivity and effectiveness. After linking CTB to AuNDs through amidation reactions, AuNDs-CTB are obtained with excellent fluorescence property, nerve target characteristic, and, particularly, neural retrograde transportation feature. The red emission of the AuNDs-CTB is well distinguished from the blue autofluorescence of normal tissues, which provides potential for detection by naked eyes. Further, the fluorescence emission intensity maintains for 10 days in vivo, suggesting great utility for long-time monitoring and sensing of the nerve tissue. Furthermore, the AuNDs-CTB with bright red fluorescence can travel through the peripheral nerve to the spinal cord rapidly by retrograde transportation. The transportation occurs for a long distance (>5 cm) within only 2 days after injection of the AuNDs-CTB into the sciatic nerve. The present study exhibits a novel method for nerve visualization and drug delivery. STATEMENT OF SIGNIFICANCE: Au nanodots (AuNDs) conjugated with cholera toxin subunit B (CTB) have been developed for nerve labeling and neural retro-transporting. The red fluorescence from AuNDs-CTB is stable in vitro (pH 4-10 and 4 h UV irradiation) and in vivo (for a long time, more than 10 days). When injecting AuNDs-CTB into the sciatic nerve located at the midpiece of the thigh, the targeted nerve emits bright red fluorescence under UV light. Furthermore, the nerve can retrograde transport the AuNDs-CTB to the spinal cord for a distance of more than 5 cm just in 2 days. This work exhibits a novel method for nerve visualization by naked eyes and demonstrates the potential for intraoperative navigation.

Simultaneous regulation of optical properties and cellular behaviors of gold nanoclusters by pre-engineering the biotemplates

Upon pre-engineering the surface charged groups of biotemplates, both optical properties and cellular behaviors of fluorescent gold nanoclusters can be simultaneously modulated.

Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters

Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.

Protein-activated transformation of silver nanoparticles into blue and red-emitting nanoclusters

Protein capping can trigger nanoparticle to nanocluster transformation at elevated pH.

Intrinsically fluorescent gold nanoclusters stabilized within a copper storage protein that follow the Irving–Williams trend in metal ion sensing

A copper storage protein is used to synthesize gold clusters with tunable emission that follow the Irving–Williams series for metal detection.