Utilization of the Pleiotropy of a Peptidic Aptamer To Fabricate Heterogeneous Nanodot-Containing Multilayer Nanostructures

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Immobilization of a carbon nanomaterial-based localized drug-release system using a bispecific material-binding peptide

Introduction

Inorganic materials are widely used in medical devices, such as artificial hearts, vessels, and joints, in stents, and as nanocarriers for drug-delivery systems. Carbon nanomaterials are of particular interest due to their biological inertness and their capability to accommodate molecules. Several attempts have been proposed, in which carbon nanomaterials are used as nanocarriers for the systemic delivery of drugs.

Materials and methods

We developed a drug-delivery system in which oxidized single-walled carbon nanohorns (oxSWNHs) were immobilized on a titanium (Ti) surface using material-binding peptides to enable localized drug delivery. For this purpose, we utilized a bispecific peptidic aptamer comprising a core sequence of a Ti-binding peptide and a SWNH-binding peptide to immobilize oxSWNHs on Ti.

Results

Scanning electron microscopy was used to confirm the presence of oxSWNHs adsorbed onto the Ti surface, and a quartz crystal microbalance was used to evaluate the binding process during oxSWNH adsorption. The oxSWNHs-ornamented Ti substrate was nontoxic to cells and released biologically active dexamethasone over a sustained period.

Conclusion

This oxSWNHs-immobilized system can be used to modify the surface of Ti in implants and be loaded with drugs that stimulate osteogenesis and bone regeneration.

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity

Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials..

Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials

The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.

Solid-binding peptides: smart tools for nanobiotechnology

Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.

High-performance scaffolds on titanium surfaces: osteoblast differentiation and mineralization promoted by a globular fibrinogen layer through cell-autonomous BMP signaling

Titanium has been widely used as a dental implant material. However, it takes several months for the implant body to bind with the jawbone. To develop new bioactive modification on titanium surfaces to achieve full osseointegration expeditiously, we used fibrinogen and fibronectin as bioactive scaffolds on the titanium plate, which are common extracellular matrix (ECM) proteins. We analyzed the features of the surface of ECM-modified titanium plates by atomic force microscopy and Fourier transform infrared spectrophotometry. We also evaluated the effect of ECM modification on promoting the differentiation and mineralization of osteoblasts on these surfaces. Fibrinogen had excellent adsorption on titanium surfaces even at low concentrations, due to the binding ability of fibrinogen via its RGD motif. The surface was composed of a fibrinogen monolayer, in which the ratio of β-sheets was decreased. Osteoblast proliferation on ECM-modified titanium surface was significantly promoted compared with titanium alone. Calcification on the modified surface was also accelerated. These ECM-promoting effects correlated with increased expression of bone morphogenetic proteins (BMPs) by the osteoblasts themselves and were inhibited by Noggin, a BMP inhibitor. These results suggest that the fibrinogen monolayer-modified titanium surface is recognized as bioactive scaffolds and promotes bone formation, resulting in the acceleration of osseointegration.

Sensitive and selective detection of thrombin by using a cyclic peptide as affinity ligand

Here we describe a sensitive assay for thrombin by using a high binding-affinity cyclic peptide against thrombin as affinity ligand. The cyclic peptide is immobilized on the magnetic beads or microplates to selectively capture thrombin. The enriched thrombin then catalyzes the cleavage of a substrate of thrombin to a detectable product. The detection of thrombin is finally achieved by measuring the generated product. This assay enables the detection of thrombin at tens fM in 100 µL of sample solution when fluorogenic substrate was applied, while detection limits reached pM level when chromogenic substrate was used. Thrombin in plasma sample can be detected with this assay. This cyclic peptide affinity ligand shows potentials for thrombin analysis in other detection formats.

Nonvolatile flash memory based on biologically integrated hierarchical nanostructures

The first six peptides of multifunctional titanium binding peptide-1 bestowed recombinant L-ferritin, minT1-LF, was genetically engineered and used to fabricate multilayered nanoparticle architecture. The multifunctionality of minT1-LF enables specific binding of nanoparticle-accommodated minT1-LF to the silicon substrate surface and wet biochemical fabrication of gate oxide layer by its biomineralization activity. Three-dimensional (3D) nanoparticle architecture with multilayered structure was fabricated by the biological layer-by-layer method and embedded in a metal oxide-semiconductor device structure as a charge storage node of a flash memory device. The 3D-integrated multilayered nanoparticle architecture successfully worked as a charge storage node in flash memory devices that exhibited improved charge storage capacity compared with that of a conventional monolayer structure device.

Universal aptamer-based real-time monitoring of enzymatic RNA synthesis

In vitro transcription is an essential laboratory technique for enzymatic RNA synthesis. Unfortunately, no methods exist for analyzing quality and quantity of the synthesized RNA while the transcription proceeds. Here we describe a simple, robust, and universal system for monitoring and quantifying the synthesis of any RNA in real time without interference from abortive transcription byproducts. The distinguishing feature is a universal fluorescence module (UFM), consisting of the eGFP-like Spinach aptamer and a highly active hammerhead ribozyme, which is appended to the RNA of interest (ROI). In the transcription mixture, the primary transcript is cleaved rapidly behind the ROI, thereby releasing always the same UFM, independent of the ROI sequence, polymerase, or promoter used. The UFM binds to the target of the Spinach aptamer, the fluorogenic dye DFHBI, and thereby induces a strong fluorescence signal. This design allows real-time quantification, standardization, parallelization, and high-throughput screening.

Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy

This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

Biologically tunable reactivity of energetic nanomaterials using protein cages

The performance of aluminum nanomaterial based energetic formulations is dependent on the mass transport, diffusion distance, and stability of reactive components. Here we use a biologically inspired approach to direct the assembly of oxidizer loaded protein cages onto the surface of aluminum nanoparticles to improve reaction kinetics by reducing the diffusion distance between the reactants. Ferritin protein cages were loaded with ammonium perchlorate (AP) or iron oxide and assembled with nAl to create an oxidation-reduction based energetic reaction and the first demonstration of a nanoscale biobased thermite material. Both materials showed enhanced exothermic behavior in comparison to nanothermite mixtures of bulk free AP or synthesized iron oxide nanopowders prepared without the use of ferritin. In addition, by utilizing a layer-by-layer (LbL) process to build multiple layers of protein cages containing iron oxide and iron oxide/AP on nAl, stoichiometric conditions and energetic performance can be optimized.

Protein nanotubes, channels and cages

Proteins are the work-horses of life and excute the essential processes involved in the growth and repair of cells. These roles include all aspects of cell signalling, metabolism and repair that allow living things to exist. They are not only chemical catalysts and machine components, they are also structural components of the cell or organism, capable of self-organisation into strong supramolecular cages, fibres and meshes. How proteins are encoded genetically and how they are sythesised in vivo is now well understood, and for an increasing number of proteins, the relationship between structure and function is known in exquisite detail. The next challenge in bionanoscience is to adapt useful protein systems to build new functional structures. Well-defined natural structures with potential useful shapes are a good starting point. With this in mind, in this chapter we discuss the properties of natural and artificial protein channels, nanotubes and cages with regard to recent progress and potential future applications. Chemistries for attaching together different proteins to form superstructures are considered as well as the difficulties associated with designing complex protein structures ab initio.

Template engineering through epitope recognition: a modular, biomimetic strategy for inorganic nanomaterial synthesis

Natural systems often utilize a single protein to perform multiple functions. Control over functional specificity is achieved through interactions with other proteins at well-defined epitope binding sites to form a variety of functional coassemblies. Inspired by the biological use of epitope recognition to perform diverse yet specific functions, we present a Template Engineering Through Epitope Recognition (TEThER) strategy that takes advantage of noncovalent, molecular recognition to achieve functional versatility from a single protein template. Engineered TEThER peptides span the biologic-inorganic interface and serve as molecular bridges between epitope binding sites on protein templates and selected inorganic materials in a localized, specific, and versatile manner. TEThER peptides are bifunctional sequences designed to noncovalently bind to the protein scaffold and to serve as nucleation sites for inorganic materials. Specifically, we functionalized identical clathrin protein cages through coassembly with designer TEThER peptides to achieve three diverse functions: the bioenabled synthesis of anatase titanium dioxide, cobalt oxide, and gold nanoparticles in aqueous solvents at room temperature and ambient pressure. Compared with previous demonstrations of site-specific inorganic biotemplating, the TEThER strategy relies solely on defined, noncovalent interactions without requiring any genetic or chemical modifications to the biomacromolecular template. Therefore, this general strategy represents a mix-and-match, biomimetic approach that can be broadly applied to other protein templates to achieve versatile and site-specific heteroassemblies of nanoscale biologic-inorganic complexes.

Spatially selective assembly of quantum dot light emitters in an LED using engineered peptides

Semiconductor nanocrystal quantum dots are utilized in numerous applications in nano- and biotechnology. In device applications, where several different material components are involved, quantum dots typically need to be assembled at explicit locations for enhanced functionality. Conventional approaches cannot meet these requirements where assembly of nanocrystals is usually material-nonspecific, thereby limiting the control of their spatial distribution. Here we demonstrate directed self-assembly of quantum dot emitters at material-specific locations in a color-conversion LED containing several material components including a metal, a dielectric, and a semiconductor. We achieve a spatially selective immobilization of quantum dot emitters by using the unique material selectivity characteristics provided by the engineered solid-binding peptides as smart linkers. Peptide-decorated quantum dots exhibited several orders of magnitude higher photoluminescence compared to the control groups, thus, potentially opening up novel ways to advance these photonic platforms in applications ranging from chemical to biodetection.

Assembly kinetics of nanocrystals via peptide hybridization

The assembly kinetics of colloidal semiconductor quantum dots (QDs) on solid inorganic surfaces is of fundamental importance for implementation of their solid-state devices. Herein an inorganic binding peptide, silica binding QBP1, was utilized for the self-assembly of nanocrystal quantum dots on silica surface as a smart molecular linker. The QD binding kinetics was studied comparatively in three different cases: first, QD adsorption with no functionalization of substrate or QD surface; second, QD adsorption on QBP1-modified surface; and, finally, adsorption of QBP1-functionalized QD on silica surface. The surface modification of QDs with QBP1 enabled 79.3-fold enhancement in QD binding affinity, while modification of a silica surface with QBP1 led to only 3.3-fold enhancement. The fluorescence microscopy images also supported a coherent assembly with correspondingly increased binding affinity. Decoration of QDs with inorganic peptides was shown to increase the amount of surface-bound QDs dramatically compared to the conventional methods. These results offer new opportunities for the assembly of QDs on solid surfaces for future device applications.

Material binding peptides for nanotechnology

Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

Direct immobilization of gold-binding antibody fragments for immunosensor applications

A novel method that enables antibody fragments to be immobilized on a sensor substrate with a high binding capability using molecular recognition has been developed. Using genetic engineering, we fabricated bispecific recombinant antibody fragments, which consist of two kinds of antibody fragments: a gold antibody fragment and a target molecule antibody fragment. Surface plasmon resonance (SPR) analysis indicated that these gold-binding bispecific antibody fragments bind directly to the gold substrate with high affinity (K(D) approximately 10(-9) M). About 70% of the bispecific antibody fragments immobilized on the gold substrate retained their target protein-binding efficiency. The Sips isotherm was used to assess the heterogeneity in antibody affinity for the bispecific antibody fragments. The results showed that the immobilized bispecific antibody fragments exhibited an increased homogeneity of affinity (K(D)) to target molecules when compared with monospecific antibody fragments immobilized by conventional methods. The use of bispecific antibody fragments to directly immobilize antibody fragments on a solid-phase substrate offers a useful platform for immunosensor applications.

Magnetic Nanofilms for Biomedical Applications

Polymeric ultrathin films, also called nanofilms or nanosheets, show peculiar properties making them potentially useful for several applications in biomedicine, e.g., as nanoplasters for localized drug release or as a new solution for closing endoluminal surgical wounds. In this sense, one of most challenging issues is film control in the working environment: the possibility of including magnetic components, such as magnetic nanoparticles or nanotubes, paves the way for the effective use of nanofilms in the human body, by allowing precise positioning by an external magnetic field. State of the art and new perspectives of magnetic nanofilms for biomedical applications are here presented, including fabrication, modeling, characterization and validation.

Site-directed delivery of ferritin-encapsulated gold nanoparticles

Newly designed porter proteins, which catch gold nanoparticles and deliver the nanoparticles selectively to a silicon dioxide (SiO(2)) surface under the specific conditions were reported. Recombinant apoferritin subunits, each of which has gold-binding peptide and titanium-binding peptide at the C- and N-terminus, respectively, can efficiently encapsulate a gold nanoparticle. The bio-conjugate, a nanogold and surrounding mutant protein subunits, had a property which can deliver itself to the SiO(2) surface through the interaction. In theory, our genetically manipulated apoferritin subunits can encapsulate gold nanoparticles of various sizes, which is a promising property for applications involving surface plasmon resonance.

Critical amino acid residues for the specific binding of the Ti-recognizing recombinant ferritin with oxide surfaces of titanium and silicon

The interactions of ferritins fused with a Ti-recognizing peptide (RKLPDA) and their mutants with titanium oxide substrates were explored with an atomic force microscope (AFM). The amino acid sequence of the peptide was systematically modified to elucidate the role of each amino acid residue in the specific interaction. Force measurements revealed a clear correlation among the sequences in the N-terminal domain of ferritin, surface potentials, and long-range electrostatic interactions. Measurements of adhesion forces clearly revealed that hydrogen bonds take part in the specific binding as well as the electrostatic interaction between charged residues and surface charges of Ti oxides. Moreover, our results indicated that not only the charged and polar residues but also a neutral residue (proline) govern the strength of the specific binding, with the order of the residues also being significant. These results demonstrate that the local structure of the peptide governs the special arrangement of charged residues and strongly affects the strength of the bindings.

Hydrodynamic transformation of a freestanding polymer nanosheet induced by a thermoresponsive surface

Freestanding quasi-two-dimensional ultrathin films (e.g., 41 nm thick polymer nanosheets) were produced, on which stimuli-responsive 47 nm thick polymer brushes were constructed by atom transfer radical polymerization (ATRP) of poly(N-isopropylacrylamide). The resulting surfaces of the multilayered polysaccharide ultrathin films were evaluated by ellipsometry, IR imaging, in situ variable-temperature atomic force microscopy (AFM), and contact angle measurements. The morphological transformation of the freestanding polymer nanosheet bearing thermoresponsive polymer brushes was observed macroscopically through reversible structural color changes at the air-water interface. The dynamic shape change of the nanosheet was also monitored with the addition of a surfactant such as sodium n-dodecylsulfate to reduce the hydrophobicity of the surface. It was then demonstrated that the highly flexible freestanding polymer nanosheet is capable of acting as a unique platform for inducing stimuli-responsive behavior in nanomaterials.

Context-dependent adsorption behavior of cyclic and linear peptides on metal oxide surfaces

Peptides with specific binding affinity to inorganic materials bridge biological systems with synthetic inorganic materials. Many inorganic-binding peptides were isolated using combinatorial peptide libraries without a good understanding of the interaction mechanism, which thus hinders the practical application of these peptides. Besides the amino acid composition, peptides' structure (e.g., cyclic structure constrained by disulfide bond) is believed to play an important role in their binding behavior. A cyclic peptide STB1 (-CHKKPSKSC-) was previously identified to electrostatically bind to TiO2 and SiO2. In the present study, the binding behavior (affinity and conformation) of STB1 and its linear version LSTB1 (-AHKKPSKSA-) on a TiO2 or SiO2 surface was investigated in three different contexts (i.e., free peptides, phage particles displaying peptides, and LacI-peptide fusion protein) using quartz crystal microbalance with energy dissipation measurement (QCM-D). The binding kinetics of STB1 and LSTB1 in the context of fusion protein to either metal oxide was quantitatively analyzed. LSTB1 showed similar binding behavior on both TiO2 and SiO2 surfaces. In the context of phage-displayed and LacI-hosted peptides, STB1 was found to have weaker binding affinity than LSTB1 for either metal oxide, but it was able to distinguish between SiO2 and TiO2. This is probably because LSTB1 has a much more flexible structure than STB1, as shown by the molecular dynamics simulation. The structural flexibility of LSTB1 enables it to explore a wider range of conformations to maximize its interaction with TiO2 and SiO2.