Design and Construction of Glutamine Binding Proteins with a Self-Adhering Capability to Unmodified Hydrophobic Surfaces as Reagentless Fluorescence Sensing Devices

A Ratiometric Organic Fluorescent Nanogel Thermometer for Highly Sensitive Temperature Sensing

Sensing temperature in biological systems is of great importance, as it is constructive to understanding various physiological and pathological processes. However, the realization of highly sensitive temperature sensing with organic fluorescent nanothermometers remains challenging. In this study, we report a ratiometric fluorescent nanogel thermometer and study its application in the determination of bactericidal temperature. The nanogel is composed of a polarity-sensitive aggregation-induced emission luminogen with dual emissions, a thermoresponsive polymer with a phase transition function, and an ionic surface with net positive charges. During temperature-induced phase transition, the nanogel exhibits a reversible and sensitive spectral change between a red-emissive state and a blue-emissive state by responding to the hydrophilic-to-hydrophobic change in the local environment. The correlation between the emission intensity ratio of the two states and the external temperature is delicately established, and the maximum relative thermal sensitivities of the optimal nanogel are determined to be 128.42 and 68.39% °C⁻¹ in water and a simulated physiological environment, respectively. The nanogel is further applied to indicate the bactericidal temperature in both visual and ratiometric ways, holding great promise in the rapid prediction of photothermal antibacterial effects and other temperature-related biological events.

Electrical Sensing of Phosphonates by Functional Coupling of Phosphonate Binding Protein PhnD to Solid-State Nanopores

Combining the stability of solid-state nanopores with the unique sensing properties of biological components in a miniaturized electrical hybrid nanopore device is a challenging approach to advance the sensitivity and selectivity of small-molecule detection in healthcare and environment analytics. Here, we demonstrate a simple method to design an electrical hybrid nanosensor comprising a bacterial binding protein tethered to a solid-state nanopore allowing high-affinity detection of phosphonates. The diverse family of bacterial substrate-binding proteins (SBPs) binds specifically and efficiently to various substances and has been implicated as an ideal biorecognition element for analyte detection in the design of hybrid bionanosensors. Here, we demonstrate that the coupling of the purified phosphonate binding protein PhnD via primary amines to the reactive NHS groups of P(DMAA-co-NMAS) polymers inside a single track-etched nanopore in poly(ethylene terephthalate) (PET) foils results in ligand-specific and concentration-dependent changes in the nanopore current. Application of the phosphonate 2-aminoethylphosphonate (2AEP) or ethylphosphonate (EP) induces a large conformational rearrangement in PnhD around the hinge in a venus flytrap mechanism resulting in a concentration depended on increase of the single pore current with binding affinities of 27 and 373 nM, respectively. Thus, the specificity and stability of this simple hybrid sensor concept combine the advantages of both, the diversity of ligand-specific substrate-binding proteins and solid-state nanopores encouraging further options to produce robust devices amenable to medical or environmental high-throughput-based applications in nanotechnology.

Sterically Shielded, Stabilized Nitrile Imine for Rapid Bioorthogonal Protein Labeling in Live Cells

In pursuit of fast bioorthogonal reactions, reactive moieties have been increasingly employed for selective labeling of biomolecules in living systems, posing a challenge in attaining reactivity without sacrificing selectivity. To address this challenge, here we report a bioinspired strategy in which molecular shape controls the selectivity of a transient, highly reactive nitrile imine dipole. By tuning the shape of structural pendants attached to the ortho position of the N-aryl ring of diaryltetrazoles-precursors of nitrile imines, we discovered a sterically shielded nitrile imine that favors the 1,3-dipolar cycloaddition over the competing nucleophilic addition. The photogenerated nitrile imine exhibits an extraordinarily long half-life of 102 s in aqueous medium, owing to its unique molecular shape that hinders the approach of a nucleophile as shown by DFT calculations. The utility of this sterically shielded nitrile imine in rapid (∼1 min) bioorthogonal labeling of glucagon receptor in live mammalian cells was demonstrated.

Engineering a periplasmic binding protein for amino acid sensors with improved binding properties

Periplasmic binding proteins (PBPs) are members of a widely distributed protein superfamily found in bacteria and archaea, and are involved in the cellular uptake of solutes. In this report, a leucine-binding PBP was engineered to detect l-Leu based on a fluorescence resonance energy transfer (FRET) change upon ligand binding. A fluorescent unnatural amino acid, l-(7-hydroxycoumarin-4-yl)ethylglycine (CouA), was genetically incorporated into the protein as a FRET donor, and a yellow fluorescent protein (YFP) was fused with its N-terminus as a FRET acceptor. When CouA was incorporated into position 178, the sensor protein showed a 2.5-fold increase in the FRET ratio. Protein engineering significantly improved its substrate specificity, showing minimal changes in the FRET ratio with the other 19 natural amino acids and d-Leu. Further modification increased the sensitivity of the sensor protein (14-fold) towards l-Leu, and it recognized l-Met as well with moderate binding affinity. Selected mutant sensors were used to measure concentrations of l-Leu in a biological sample (fetal bovine serum) and to determine the optical purity of Leu and Met. This FRET-based sensor design strategy allowed us to easily manipulate the natural receptor to improve its binding affinity and specificity and to recognize other natural molecules, which are not recognized by the wild-type receptor. The design strategy can be applied to other natural receptors, enabling engineering receptors that sense biochemically interesting molecules.

Intracellular temperature measurements with fluorescent polymeric thermometers

Intracellular temperature can be measured using fluorescent polymeric thermometersviatheir temperature-dependent fluorescence signals.

Genetically encoded FRET sensors using a fluorescent unnatural amino acid as a FRET donor

FRET sensors based on fluorescent proteins have been powerful tools for probing protein–protein interactions and structural changes within proteins.

Strong solvent dependence of linear and non-linear optical properties of donor–acceptor type pyrrolo[3,2-b]pyrroles

The pyrrolo[3,2-b]pyrrole core was determined to be an efficient linker allowing the conjugation of peripheral benzene rings. The resulting dipolar compounds displayed strong solvatochromism of fluorescence.

From fluorescence polarization to Quenchbody: Recent progress in fluorescent reagentless biosensors based on antibody and other binding proteins

Recently, antibody-based fluorescent biosensors are receiving considerable attention as a suitable biomolecule for diagnostics, namely, homogeneous immunoassay and also as an imaging probe. To date, several strategies for "reagentless biosensors" based on antibodies and natural and engineered binding proteins have been described. In this review, several approaches are introduced including a recently described fluorescent antibody-based biosensor Quenchbody, which works on the principle of fluorescence quenching of attached dye and its antigen-dependent release. The merits and possible demerits of each approach are discussed. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.

Emerging applications of multifunctional elastin-like recombinamers

Elastin-like recombinamers have grown in popularity in the field of protein-inspired biomimetic materials and have found widespread use in biomedical applications. Modern genetic-engineering techniques have allowed the design of multifunctional materials with an extraordinary control over their architecture and physicochemical properties, such as stimuli-responsiveness, monodispersity, biocompatibility or self-assembly, amongst others. Indeed, these materials are playing an increasingly important role in a diverse range of applications, such as drug delivery, tissue engineering and 'smart' systems. Herein, we review some of the most interesting examples of recent advances and progressive applications of elastin-like recombinamers in biomaterial and nano-engineering sciences in recent years.

Environmentally sensitive fluorescent sensors based on synthetic peptides

Biosensors allow the direct detection of molecular analytes, by associating a biological receptor with a transducer able to convert the analyte-receptor recognition event into a measurable signal. We review recent work aimed at developing synthetic fluorescent molecular sensors for a variety of analytes, based on peptidic receptors labeled with environmentally sensitive fluorophores. Fluorescent indicators based on synthetic peptides are highly interesting alternatives to protein-based sensors, since they can be synthesized chemically, are stable, and can be easily modified in a site-specific manner for fluorophore coupling and for immobilization on solid supports.

Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae

Here, we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), can be genetically incorporated into proteins in yeast with excellent selectivity and efficiency by means of an orthogonal tRNA/aminoacyl-tRNA synthetase pair. This small, environmentally sensitive fluorophore was site-specifically incorporated into Escherichia coli glutamine binding protein and used to directly probe local structural changes caused by ligand binding. The small size of Anap and the ability to introduce it by simple mutagenesis at defined sites in the proteome make it a useful local probe of protein structure, molecular interactions, protein folding, and localization.

Recombinamers: combining molecular complexity with diverse bioactivities for advanced biomedical and biotechnological applications

The rapid development of polymer science has led to literally thousands of different monomers and an almost endless number of possibilities arising from their combination. The most promising strategy to date has been to consider natural products as macromolecules that provide the best option for obtaining functional materials. Proteins, with their high levels of complexity and functionality, are one of the best examples of this approach. In addition, the development of genetic engineering has permitted the design and highly controlled synthesis of proteinaceous materials with complex and advanced functionalities. Elastin-like recombinamers (ELRs) are presented herein as an example of an extraordinary convergence of different properties that is not found in any other synthetic polymer system. These materials are highly biocompatible, stimuli-responsive, show unusual self-assembly properties, and can incorporate bioactive domains and other functionalities along the polypeptide chain. These attributes are an important factor in the development of biomedical and biotechnological applications such as tissue engineering, drug delivery, purification of recombinant proteins, biosensors or stimuli-responsive surfaces.

Pseudoenzymatic dealkylation of alkyltins by biological dithiols

We investigated the time dependence of the degradation of three alkyltin derivatives by a nine amino acid linear peptide (I(1)LGCWCYLR(9)) containing a CXC motif derived from the primary sequence of stannin, a membrane protein involved in alkyltin toxicity. We monitored the reaction kinetics using the intrinsic fluorescence of the tryptophan residue in position 5 of the peptide and found that all of the alkyltins analyzed are progressively degraded to dialkyl derivatives, following a pseudoenzymatic reaction mechanism. The end point of the reactions is the formation of a covalent complex between the disubstituted alkyltin and the peptide cysteines. These data agree with the speciation profiles proposed for polysubstituted alkyltins in the environment and reveal a possible biotic degradation pathway for these toxic compounds.

Cell-bionics: tools for real-time sensor processing

The accurate monitoring of the physiological status of cells, tissues and whole organisms demands a new generation of devices capable of providing accurate data in real time with minimal perturbation of the system being measured. To deliver on the promise of cell-bionics advances over the past decade in miniaturization, analogue signal processing, low-power electronics, materials science and protein engineering need to be brought together. In this paper we summarize recent advances in our research that is moving us in this direction. Two areas in particular are highlighted: the exploitation of the physical properties inherent in semiconductor devices to perform very low power on chip signal processing and the use of gene technology to tailor proteins for sensor applications. In the context of engineered tissues, cell-bionics could offer the ability to monitor the precise physiological state of the construct, both during 'manufacture' and post-implantation. Monitoring during manufacture, particularly by embedded devices, would offer quality assurance of the materials components and the fabrication process. Post-implantation monitoring would reveal changes in the underlying physiology as a result of the tissue construct adapting to its new environment.

Reversible fluorescence quenching in carbon nanotubes for biomolecular sensing

Biosensing applications of single-walled carbon nanotubes have been demonstrated in solid-state device structures. Bioanalyte sensing schemes based on coupling of reversible nanotube fluorescence quenching to redox reactions paired to enzymatic peroxide generation have also been pursued. Here we show a new approach to highly sensitive nanotube-based optical sensing. Single-walled carbon nanotubes interacting with dye-ligand conjugates--a redox-active dye molecule that is covalently bound to a biological receptor ligand (such as biotin in this case)--showed fluorescence quenching. Further interaction between the receptor ligand on the conjugates and target analytes (avidin in this case) induced the recovery of the quenched fluorescence, forming the basis of the sensing scheme. Nanomolar sensitivity was attained with high specificity for the target analyte. This is a versatile approach because a wide range of conjugation possibilities exists between the potential receptors and redox quenchers.

A reagentless optical biosensor based on the intrinsic absorption properties of peroxidase

During the reversible reaction between peroxidase (HRP) and H(2)O(2), several peroxidase intermediate species, showing different molecular absorption spectra, are formed which can be used for H(2)O(2) determination; when H(2)O(2) is generated in a previous enzymatic reaction, the substrate involved in this reaction can also be determined. On this basis, a new family of fully reversible reagentless optical biosensors containing HRP is presented; glucose determination is used as a model. The biosensor (which can be used for at least 6 months and/or more than 750 measurements) is prepared by HRP and glucose oxidase entrapment in a polyacrylamide gel matrix. A mathematical model (in which optical, kinetic and transport aspects are considered) relating the measured absorbance with the substrate concentration is also presented together with a simple methodology for characterization of this kind of biosensor. Regarding the optical model, the Kubelka-Mulk theory of reflectance does not give good results and the biosensors are better described by the Rayleigh theory of polymer solutions. Under working conditions, linear response ranges from 1.5x10(-6) to 3.0x10(-4)M glucose and CV was about 4%. This biosensor has been applied for glucose determination in fruit juices and synthetic serum samples without sample pretreatment.

Using blood hemoglobin for blood analysis

This paper demonstrates that the spectrophotometric properties of blood hemoglobin (Hb) can be used for the direct determination of biochemical compounds in blood. Glucose is used as a model, but the methodology can be applied to many other compounds (only a previous enzymatic reaction producing H(2)O(2) is needed). In order to develop the method, a model relating the Hb absorbance variation during the reaction with the glucose concentration has been developed to provide theoretical support for the method and to predict its application to other compounds. In addition, clear blood samples need to be prepared without pre-treatment and lateral reactions of H(2)O(2) with other blood constituents need to be blocked; this has been achieved with 100 : 1 v/v blood dilution in bi-distilled water and azide addition. The linear response range of the method can be fitted between 2 and 540 mg dL(-1) glucose relative to the original blood sample (RSD about 4%, 70 mg dL(-1)). The analyte concentration can be obtained by an absolute calibration method or by the standard addition method; both have been applied for direct glucose determination in several blood samples and good correlations with those obtained by an automatic analyzer have been obtained.

Fabrication of an antibody microwell array with self-adhering antibody binding protein

One of the promising methods of preparing antibody arrays is immobilizing antibodies with protein A or protein G, each of which binds specifically to the heavy chain constant (Fc) region of immunoglobulin G (IgG). In this system, antibody immobilization efficiency depends on the number of active Fc binding proteins that need to be immobilized on the surface. Here we have designed and constructed an Fc binding protein with a self-adhering ability that can be immobilized on the hydrophobic surface by simple adsorption. It consists of an Fc binding domain of protein G (G3) and hydrophobic domain of elastin (E72). Direct observation revealed its self-adhering ability on the hydrophobic surface. The enzyme-linked immunosorbent assay (ELISA) showed that it retained antibody binding ability on the surface. The antibody array model was prepared on a hydrophobic microwell glass slide with E72G3, which specifically detect the antigen with a sevenfold greater sensitivity than the G3-treated slide. These results suggest that the E72G3 is useful for simple and effective immobilization of antibodies and can be used to fabricate any immuno devices.

Maltose-binding protein: a versatile platform for prototyping biosensing

The bacterial periplasmic-binding protein (PBP) superfamily members, in particular the maltose-binding protein, have been used extensively to prototype a variety of biosensing platforms. Although quite diverse at the primary sequence level, this protein superfamily retains the same basic two-domain structure, and upon binding a recognized ligand almost all PBPs undergo a conformational change to a closed structure. This process forms the basis for most, but not all, PBP-based biosensor signal transduction. Many direct detection or reagentless sensing modalities have been utilized with maltose-binding protein for both in vitro and in vivo detection of target compounds. Signal transduction modalities developed to date include direct fluorescence, electrochemical detection, fluorescence resonance energy transfer (FRET)-based detection, surface-tethered FRET sensing, hybrid quantum dot FRET sensing, and enzymatic detection, each of which have different benefits, potential applications and limitations.

Periplasmic binding proteins: a versatile superfamily for protein engineering

The diversity of biological function, ligand binding, conformational changes and structural adaptability of the periplasmic binding protein superfamily have been exploited to engineer biosensors, allosteric control elements, biologically active receptors and enzymes using a combination of techniques, including computational design. Extensively redesigned periplasmic binding proteins have been re-introduced into bacteria to function in synthetic signal transduction pathways that respond to extracellular ligands and as biologically active enzymes.