Genetically Induced In Situ-Poling for Piezo-Active Biohybrid Nanowires

Functional mimicry of sea urchin biomineralization proteins with CaCO3-binding peptides selected by phage display

The intricate process of biomineralization, e.g. in sea urchins, involves the precise interplay of highly regulated mineralization proteins and the spatiotemporal coordination achieved through compartmentalization. However, the investigation of biomineralization effector molecules, e.g. proteins, is challenging, due to their very low abundance. Therefore, we investigate the functional mimicry in the bioinspired precipitation of calcium carbonate (CaCO3) with artificial peptides selected from a peptide library by phage display based on peptide-binding to calcite and aragonite, respectively. The structure-directing effects of the identified peptides were compared to those of natural protein mixes isolated from skeletal (test) structures of two sea urchin species (Arbacia lixula and Paracentrotus lividus). The calcium carbonate samples deposited in the absence or presence of peptides were analyzed with a set of complementary techniques with regard to morphology, polymorph, and nanostructural motifs. Remarkably, some of the CaCO3-binding peptides induced morphological features in calcite that appeared similar to those obtained in the presence of the natural protein mixes. Many of the peptides identified as most effective in exerting a structure-directing effect on calcium carbonate crystallization were rich in basic amino acid residues. Hence, our in vitro mineralization study further highlights the important, but often neglected, role of positively charged soluble organic matrices associated with biological and bioinspired CaCO3 deposition.

A New Strategy for Microbial Taxonomic Identification through Micro-Biosynthetic Gold Nanoparticles and Machine Learning

Microorganisms can serve as biological factories for the synthesis of inorganic nanomaterials that can become useful as nanocatalysts, energy-harvesting-storage components, antibacterial agents, and biomedical materials. Herein, the development of biosynthesis of inorganic nanomaterials into a simple, stable, and accurate strategy for distinguishing microorganisms from multiple classification levels (i.e., kingdom, order, genus, and species) without gene amplification, biochemical testing, or target recognition is reported. Gold nanoparticles (AuNPs) biosynthesized by different microorganisms differ in color of the solution, and their features can be characterized, including the particle size, the surface plasmon resonance (SPR) spectrum, and the surface potential. The inter-relation between the features of micro-biosynthetic AuNPs and the classification of microorganisms are exploited at different levels through machine learning to establish a taxonomic model. This model agrees well with traditional classification methods that offers a new strategy for microbial taxonomic identification. The underlying mechanism of this strategy is related to the biomolecules produced by different microorganisms including glucose, glutathione, and nicotinamide adenine dinucleotide phosphate-dependent reductase that regulate the features of micro-biosynthetic AuNPs. This work broadens the application of biosynthesis of inorganic materials through micro-biosynthetic AuNPs and machine learning, which holds great promise as a tool for biomedical research.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

Engineered Bacteriophages for Practical Applications

The diversity of advanced genetic engineering techniques that have become available in recent years has enabled a more precise manipulation of genes and genomes. Among these, bacteriophage genomes stand out as an interesting target due to their dependence on a host for replication, which previously complicated their manipulation, and due as well to the many possible fields in which they can be used. In this review, we highlight recent applications for which genetically modified bacteriophages are being employed: as phage therapy in medicine, animal industries and agricultural settings; as a source of new antimicrobials; as biosensors for research, health and environmental purposes; and as genetic engineering tools themselves.

Biosynthesis of inorganic nanomaterials using microbial cells and bacteriophages

Inorganic nanomaterials are widely used in chemical, electronics, photonics, energy and medical industries. Preparing a nanomaterial (NM) typically requires physical and/or chemical methods that involve harsh and environmentally hazardous conditions. Recently, wild-type and genetically engineered microorganisms have been harnessed for the biosynthesis of inorganic NMs under mild and environmentally friendly conditions. Microorganisms such as microalgae, fungi and bacteria, as well as bacteriophages, can be used as biofactories to produce single-element and multi-element inorganic NMs. This Review describes the emerging area of inorganic NM biosynthesis, emphasizing the mechanisms of inorganic-ion reduction and detoxification, while also highlighting the proteins and peptides involved. We show how analysing a Pourbaix diagram can help us devise strategies for the predictive biosynthesis of NMs with high producibility and crystallinity and also describe how to control the size and morphology of the product. Here, we survey biosynthetic inorganic NMs of 55 elements and their applications in catalysis, energy harvesting and storage, electronics, antimicrobials and biomedical therapy. Furthermore, a step-by-step flow chart is presented to aid the design and biosynthesis of inorganic NMs employing microbial cells. Future research in this area will add to the diversity of available inorganic NMs but should also address scalability and purity.

Recent Developments and Prospects of M13- Bacteriophage Based Piezoelectric Energy Harvesting Devices

Recently, biocompatible energy harvesting devices have received a great deal of attention for biomedical applications. Among various biomaterials, viruses are expected to be very promising biomaterials for the fabrication of functional devices due to their unique characteristics. While other natural biomaterials have limitations in mass-production, low piezoelectric properties, and surface modification, M13 bacteriophages (phages), which is one type of virus, are likely to overcome these issues with their mass-amplification, self-assembled structure, and genetic modification. Based on these advantages, many researchers have started to develop virus-based energy harvesting devices exhibiting superior properties to previous biomaterial-based devices. To enhance the power of these devices, researchers have tried to modify the surface properties of M13 phages, form biomimetic hierarchical structures, control the dipole alignments, and more. These methods for fabricating virus-based energy harvesting devices can form a powerful strategy to develop high-performance biocompatible energy devices for a wide range of practical applications in the future. In this review, we discuss all these issues in detail.

Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays

This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC₅₀), binding affinity (K_i), and binding free energy (ΔG_ads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.

Genetically Modified M13 Bacteriophage Nanonets for Enzyme Catalysis and Recovery

Enzyme-based biocatalysis exhibits multiple advantages over inorganic catalysts, including the biocompatibility and the unchallenged specificity of enzymes towards their substrate. The recovery and repeated use of enzymes is essential for any realistic application in biotechnology, but is not easily achieved with current strategies. For this purpose, enzymes are often immobilized on inorganic scaffolds, which could entail a reduction of the enzymes’ activity. Here, we show that immobilization to a nano-scaled biological scaffold, a nanonetwork of end-to-end cross-linked M13 bacteriophages, ensures high enzymatic activity and at the same time allows for the simple recovery of the enzymes. The bacteriophages have been genetically engineered to express AviTags at their ends, which permit biotinylation and their specific end-to-end self-assembly while allowing space on the major coat protein for enzyme coupling. We demonstrate that the phages form nanonetwork structures and that these so-called nanonets remain highly active even after re-using the nanonets multiple times in a flow-through reactor.

Self-Assembled Phage-Based Colloids for High Localized Enzymatic Activity

Catalytically active colloids are model systems for chemical motors and active matter. It is desirable to replace the inorganic catalysts and the toxic fuels that are often used with biocompatible enzymatic reactions. However, compared to inorganic catalysts, enzyme-coated colloids tend to exhibit less activity. Here, we show that the self-assembly of genetically engineered M13 bacteriophages that bind enzymes to magnetic beads ensures high and localized enzymatic activity. These phage-decorated colloids provide a proteinaceous environment for directed enzyme immobilization. The magnetic properties of the colloidal carrier particle permit repeated enzyme recovery from a reaction solution, while the enzymatic activity is retained. Moreover, localizing the phage-based construct with a magnetic field in a microcontainer allows the enzyme-phage-colloids to function as an enzymatic micropump, where the enzymatic reaction generates a fluid flow. This system shows the fastest fluid flow reported to date by a biocompatible enzymatic micropump. In addition, it is functional in complex media including blood, where the enzyme-driven micropump can be powered at the physiological blood-urea concentrations.