Optical determination of glutamine using a genetically engineered protein

Structural features of the glutamate-binding protein from Corynebacterium glutamicum

L-glutamate (Glu) is the major excitatory transmitter in mammalian brain. Inadequate concentration of Glu in the brain correlates to mood disorder. In industry, Glu is used as a flavour enhancer in food and in foodstuff processing. A high concentration of Glu has several effects on human health such as hypersensitive effects, headache and stomach pain. The presence of Glu in food can be detected by different analytical methods based on chromatography, or capillary electrophoresis or amperometric techniques. We have isolated and characterized a glutamate-binding protein (GluB) from the Gram-positive bacteria Corynebacterium glutamicum. Together with GluC protein, GluD protein and the cytoplasmic protein GluA, GluB permits the transport of Glu in/out of cell. In this study, we have investigated the binding features of GluB as well as the effect of temperature on its structure both in the absence and in the presence of Glu. The results have showed that GluB has a high affinity and selectivity versus Glu (nanomolar range) and the presence of the ligand induces a higher thermal stability of the protein structure.

Engineering a switch-based biosensor for arginine using a Thermotoga maritima periplasmic binding protein

The Thermotoga maritima arginine-binding protein (TmArgBP) has been modified to create a reagentless fluorescent protein biosensor. Two design methods for biosensor construction are compared: 1) solvent accessibility of environmentally-sensitive probes and 2) fluorescence deactivation due to photo-induced electron transfer (PET). Nine single cysteine TmArgBP mutants were created and labeled with three different environmentally sensitive fluorescent probes. These mutants demonstrated limited changes in fluorescence emission upon the addition of arginine. In contrast, the PET-based biosensor provides significant enhancements over the traditional approach and provides a fluorescence quenching mechanism that was capable of providing quantitative detection of arginine. Site-directed mutagenesis of TmArgBP was used to create attachment points for the fluorescent probe (K145C) and for an internal aromatic residue (D18X) to serve as the PET quencher. Both tyrosine and tryptophan, but not phenylalanine, were able to quench the emission of the fluorescent probe by more than 80% upon the addition of arginine. The dissociation constant for arginine ranged from 0.87 to 1.5 μM across the different sensors. This PET-based strategy provides a simple and broadly applicable approach for the analytical detection of small molecules that may be applied to any protein that exhibits conformational switching in a ligand dependent manner.

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.

A novel glutamine biosensor based on zinc oxide nanorod and glutaminase enzyme from Hypocria jecorina

A novel biosensor for determination of L-glutamine in pharmaceutical glutamine powder was developed via immobilizing our produced glutaminase enzyme from Hypocria jecorina onto our prepared zinc oxide (ZnO) nanorod and chitosan. ZnO nanorods were prepared as surface-dependent and surface-independent and both were used. The biosensor is specific for L-glutamine and the peculiar analytical properties (linearity range, reproducibility, and accuracy) of it were experimentally determined. The optimum operating conditions of the biosensor such as buffer concentration, buffer pH, and medium temperature effect on the response of biosensor were studied. Km and Vmax values for the our-producing glutaminase enzyme from Hypocria jecorina immobilized on the biosensor were also determined as 0.29 mM and 208.33 mV/min., respectively, from Lineweaver-Burk plot. The biosensor was then used for the determination of glutamine contained in pharmaceutical formulations.

FIBS-enabled noninvasive metabolic profiling

In the era of computational biology, new high throughput experimental systems are necessary in order to populate and refine models so that they can be validated for predictive purposes. Ideally such systems would be low volume, which precludes sampling and destructive analyses when time course data are to be obtained. What is needed is an in situ monitoring tool which can report the necessary information in real-time and noninvasively. An interesting option is the use of fluorescent, protein-based in vivo biological sensors as reporters of intracellular concentrations. One particular class of in vivo biosensors that has found applications in metabolite quantification is based on Förster Resonance Energy Transfer (FRET) between two fluorescent proteins connected by a ligand binding domain. FRET integrated biological sensors (FIBS) are constitutively produced within the cell line, they have fast response times and their spectral characteristics change based on the concentration of metabolite within the cell. In this paper, the method for constructing Chinese hamster ovary (CHO) cell lines that constitutively express a FIBS for glucose and glutamine and calibrating the FIBS in vivo in batch cell culture in order to enable future quantification of intracellular metabolite concentration is described. Data from fed-batch CHO cell cultures demonstrates that the FIBS was able in each case to detect the resulting change in the intracellular concentration. Using the fluorescent signal from the FIBS and the previously constructed calibration curve, the intracellular concentration was accurately determined as confirmed by an independent enzymatic assay.

Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein

The Thermotoga maritima arginine binding protein (TmArgBP) is a member of the periplasmic binding protein superfamily. As a highly thermostable protein, TmArgBP has been investigated for the potential to serve as a protein scaffold for the development of fluorescent protein biosensors. To establish a relationship between structural dynamics and ligand binding capabilities, we constructed single tryptophan mutants to probe the arginine binding pocket. Trp residues placed around the binding pocket reveal a strong dependence on fluorescence emission of the protein with arginine for all but one of the mutants. Using these data, we calculated dissociation constants of 1.9-3.3 μM for arginine. Stern-Volmer quenching analysis demonstrated that the protein undergoes a large conformational change upon ligand binding, which is a common feature of this protein superfamily. While still active at room temperature, time-resolved intensity and anisotropy decay data suggest that the protein exists as a highly rigid structure under these conditions. Interestingly, TmArgBP exists as a dimer at room temperature in both the presence and absence of arginine, as determined by asymmetric flow field flow fractionation (AF4) and supported by native gel-electrophoresis and time-resolved anisotropy. Our data on dynamics and stability will contribute to our understanding of hyperthermophilic proteins and their potential biotechnological applications.

Development of a novel fluorescent protein construct by genetically fusing green fluorescent protein to the N-terminal of aspartate dehydrogenase

We developed a fluorescent protein construct by genetically fusing green fluorescent protein (GFP) to aspartate dehydrogenase from Thermotoga maritima. The fusion protein was cloned, heterologously expressed in Escherichia coli cells, and purified by Ni-chelate affinity chromatography. It was then introduced into a measurement cuvette to monitor its fluorescence signal. Aspartate dehydrogenase functioned as the biorecognition element, and aspartate-induced conformational change was converted to a fluorescence signal by GFP. The recombinant protein responded to l-aspartate (l-Asp) linearly within the concentration range of 1-50 mM, and it was capable of giving a fluorescence signal in 1 Min. Although a linear response was also observed for l-Glu, the fluorescence signal was 2.7 times lower than that observed for l-Asp. In the present study, we describe two novelties: development of a genetically encoded fluorescent protein construct for monitoring of l-Asp in vitro, and employment of aspartate dehydrogenase scaffold as a biorecognition element. A few genetically encoded amino-acid biosensors have been described in the literature, but to our knowledge, a protein has not been constructed solely for determination of l-Asp. Periplasmic ligand binding proteins offer high binding affinity in the micromolar range, and they are frequently used as biorecognition elements. Instead of choosing a periplasmic l-Asp binding protein, we attempted to use the substrate specificity of aspartate dehydrogenase enzyme.

Production and optimization of L-glutaminase enzyme from Hypocrea jecorina pure culture

L-Glutaminase (L-glutamine amidohydrolase, EC 3.5.1.2) is the important enzyme that catalyzes the deamination of L-glutamine to L-glutamic acid and ammonium ions. Recently, L-glutaminase has received much attention with respect to its therapeutic and industrial applications. It acts as a potent antileukemic agent and shows flavor-enhancing capacity in the production of fermented foods. Glutaminase activity is widely distributed in plants, animal tissues, and microorganisms, including bacteria, yeasts, and fungi. This study presents microbial production of glutaminase enzyme from Hypocrea jecorina pure culture and determination of optimum conditions and calculation of kinetic parameters of the produced enzyme. The optimum values were determined by using sa Nesslerization reaction for our produced glutaminase enzyme. The optimum pH value was determined as 8.0 and optimum temperature as 50°C for the glutaminase enzyme. The Km and Vmax values, the kinetic parameters, of enzyme produced from Hypocrea jecorina, pure culture were determined as 0.491 mM for Km and 13.86 U/L for Vmax by plotted Lineweaver-Burk graphing, respectively. The glutaminase enzyme from H. jecorina microorganism has very high thermal and storage stability.

Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story

Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritima with a particular eye on its potential biotechnological applications.

In situ monitoring of intracellular glucose and glutamine in CHO cell culture

The development of processes to produce biopharmaceuticals industrially is still largely empirical and relies on optimizing both medium formulation and cell line in a product-specific manner. Current small-scale (well plate-based) process development methods cannot provide sufficient sample volume for analysis, to obtain information on nutrient utilization which can be problematic when processes are scaled to industrial fermenters. We envision a platform where essential metabolites can be monitored non-invasively and in real time in an ultra-low volume assay in order to provide additional information on cellular metabolism in high throughput screens. Towards this end, we have developed a model system of Chinese Hamster Ovary cells stably expressing protein-based biosensors for glucose and glutamine. Herein, we demonstrate that these can accurately reflect changing intracellular metabolite concentrations in vivo during batch and fed-batch culture of CHO cells. The ability to monitor intracellular depletion of essential nutrients in high throughput will allow rapid development of improved bioprocesses.

Fluorescence-based biosensors

The field of optical sensors has been a growing research area over the last three decades. A wide range of books and review articles has been published by experts in the field who have highlighted the advantages of optical sensing over other transduction methods. Fluorescence is by far the method most often applied and comes in a variety of schemes. Nowadays, one of the most common approaches in the field of optical biosensors is to combine the high sensitivity of fluorescence detection in combination with the high selectivity provided by ligand-binding proteins. In this chapter we deal with reviewing our recent results on the implementation of fluorescence-based sensors for monitoring environmentally hazardous gas molecules (e.g. nitric oxide, hydrogen sulfide). Reflectivity-based sensors, fluorescence correlation spectroscopy-based (FCS) systems, and sensors relying on the enhanced fluorescence emission on silver island films (SIFs) coupled to the total internal reflection fluorescence mode (TIRF) for the detection of gliadin and other prolamines considered toxic for celiac patients are also discussed herein.

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscopic observations with specific secondary structural elements. The data determined the presence of a buried beta-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding of bacterial binding protein family members and their potential biotechnological applications.

A biosensor for fluorescent determination of ADP with high time resolution

Nearly every cellular process requires the presence of ATP. This is reflected in the vast number of enzymes like kinases or ATP hydrolases, both of which cleave the terminal phosphate from ATP, thereby releasing ADP. Despite the fact that ATP hydrolysis is one of the most fundamental reactions in biological systems, there are only a few methods available for direct measurements of enzymatic-driven ATP conversion. Here we describe the development of a reagentless biosensor for ADP, the common product of all ATPases and kinases, which allows the real-time detection of ADP, produced enzymatically. The biosensor is derived from a bacterial actin homologue, ParM, as protein framework. A single fluorophore (a diethylaminocoumarin), attached to ParM at the edge of the nucleotide binding site, couples ADP binding to a >3.5-fold increase in fluorescence intensity. The labeled ParM variant has high affinity for ADP (0.46 μm) and a fast signal response, controlled by the rate of ADP binding to the sensor (0.65 μm⁻¹s⁻¹). Amino acids in the active site were mutated to reduce ATP affinity and achieve a >400-fold discrimination against triphosphate binding. A further mutation ensured that the final sensor did not form filaments and, as a consequence, has extremely low ATPase activity. The broad applicability of N-[2-(1-maleimidyl)ethyl]-7-diethylaminocoumarin-3-carboxamide (MDCC)-ParM as a sensitive probe for ADP is demonstrated in real-time kinetic assays on two different ATPases and a protein kinase.

On the design of low-cost fluorescent protein biosensors

There is a large body of knowledge on proteins and their ligands that is available to the sensor researcher for the successful design of fluorescent biosensors. Chemically synthesized receptors rarely match the sensitivity and selectivity of proteins.Additionally, proteins are easily produced and manipulated through recombinant protein techniques. Although limitations exist in the prediction of signal response of proteins labeled with fluorescent probes, thoughtful experimentation can lead to useful, highly responsive fluorescent protein assays. Conversion of these assays into sensor devices may require additional manipulation of the fluorescence properties of the labeled proteins. We have shown that this can be achieved by a second fluorophore serving as a reference for ratiometric measurements. The choice of reference is contingent on the low-cost, miniaturized design of the device. Accordingly, the reference fluorophore is excitable with the same LED as the signal transducing probe and has a fluorescence decay lifetime that is orders of magnitude longer.Alternating illumination with intensity modulated light at two frequencies allows for ratiometric sensing without the need for bulky filter wheels while collecting the signals over a wide range of emission wavelengths. The result is a simple optoelectronics design that is cost-effective and small enough to be portable.In summary, the process of designing protein-based fluorescent biosensors for practical applications requires the systematic collaboration of a cross-disciplinary group of molecular biologists, chemists and engineers.

Protein conformational changes revealed by optical spectroscopic reflectometry in porous silicon multilayers

The protein-ligand molecular interactions imply strong geometrical and structural rearrangements of the biological complex which are normally detected by high sensitivity optical techniques such as time-resolved fluorescence microscopy. In this work, we have measured, by optical spectroscopic reflectometry in the visible-near-infrared region, the interaction between a sugar binding protein (SBP), covalently bound on the surface of a porous silicon (PSi) microcavity, and glucose, at different concentrations and temperatures. Variable-angle spectroscopic ellipsometric (VASE) characterization of protein-functionalized PSi layers confirms that the protein-ligand system has an overall volume smaller than the SBP alone.

Low-cost optical lifetime assisted ratiometric glutamine sensor based on glutamine binding protein

Here we report a reagentless fluorescence sensing technique for glutamine in the submicromolar range based on the glutamine binding protein (QBP). The S179C mutant is labeled with the short-lived acrylodan (lifetime<5ns) and the long-lived tris(dibenzoylmethane) mono(5-amino-1,10-phenanthroline)europium(III) (lifetime > 300 micros) at the -SH and the N-terminal positions, respectively. In the presence of glutamine the fluorescence of acrylodan is quenched, while the fluorescence of europium complex remains constant. In this report we describe an innovative technique, the so called lifetime assisted ratiometric sensing to discriminate the two fluorescence signals using minimal optics and power requirements. This method exploits the large difference between the fluorescence lifetimes of the two fluorophores to isolate the individual fluorescence from each other by alternating the modulation frequency of the excitation light between 300 Hz and 10 kHz. The result is a ratiometric optical method that does not require expensive and highly attenuating band pass filters for each of the dyes, but only one long pass filter for both. Thus, the signal to noise ratio is enhanced, and at the same time, the optical setup is simplified. The end product is a simple sensing device suitable for low-cost applications such as point-of-care diagnostics or in-the-field analysis.

Comparing the performance of the optical glucose assay based on glucose binding protein with high-performance anion-exchange chromatography with pulsed electrochemical detection: efforts to design a low-cost point-of-care glucose sensor

BACKGROUND

The glucose binding protein (GBP) is one of many soluble binding proteins found in the periplasmic space of gram-negative bacteria. These proteins are responsible for chemotactic responses and active transport of chemical species across the membrane. Upon ligand binding, binding proteins undergo a large conformational change, which is the basis for converting these proteins into optical biosensors.

METHODS

The GBP biosensor was prepared by attaching a polarity-sensitive fluorescent probe to a single cysteine mutation at a site on the protein that is allosterically responsive to glucose binding. The fluorescence response of the resulting sensor was validated against high-performance anion-exchange chromatography (HPAEC) with pulsed electrochemical detection. Finally, a simple fluorescence reader was built using a lifetime-assisted ratiometric technique.

RESULTS

The GBP assay has a linear range of quantification of 0.100-2.00 microM and a sensitivity of 0.164 microM(-1) under the specified experimental conditions. The comparison between GBP and HPAEC readings for nine blind samples indicates that there is no statistical difference between the analytical results of the two methods at the 95% confidence level. Although the methods of fluorescence detection are based on different principles, the response of the homemade device to glucose concentrations was comparable to the response of the larger and more expensive tabletop fluorescence spectrophotometer.

CONCLUSIONS

A glucose binding protein labeled with a polarity-sensitive probe can be used for measuring micromolar amounts of glucose. Using a lifetime-assisted ratiometric technique, a low-cost GBP-based micromolar glucose monitor could be built.

Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein

We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstrom resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 +/- 1 degrees C and 144 +/- 2 degrees C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C*Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.

Branched-chain Amino Acid Biosensing Using Fluorescent Modified Engineered Leucine/Isoleucine/Valine Binding Protein

A novel fluorescence sensing system for branched-chain amino acids (BCAAs) was developed based on engineered leucine/isoleucine/valine-binding proteins (LIVBPs) conjugated with environmentally sensitive fluorescence probes. LIVBP was cloned from Escherichia coli and Gln149Cys, Gly227Cys, and Gln254Cys mutants were generated by genetic engineering. The mutant LIVBPs were then modified with environmentally sensitive fluorophores. Based on the fluorescence intensity change observed upon the binding of the ligands, the MIANS-conjugated Gln149Cys mutant (Gln149Cys-M) showed the highest and most sensitive response. The BCAAs Leu, Ile, and Val can each be monitored at the sub-micromolar level using Gln149Cys-M. Measurements were also carried out on a mixture of BCAFAs and revealed that Gln149Cys-M-based measurement is not significantly affected by the change in the molar ratio of Leu, Ile and Val in the sample. Its high sensitivity and group-specific molecular recognition ability make the new sensing system ideally suited for the measurement of BCAAs and the determination of the Fischer ratio, an indicator of hepatic disease involving metabolic dysfunction.

Visualization of Arginine Influx into Plant Cells Using a Specific FRET-sensor

Amino acids are not only the building blocks of proteins, but are the metabolic precursors of a variety of primary and secondary metabolites. In order to detect and visualize how plants transport, sense, and store amino acids with sub-cellular specificity, chimeric fluorescent proteins that respond to changes in amino acid concentrations were constructed. The reporter element of these sensors consists of a periplasmic bacterial protein that undergoes large, non-enzymatic conformational changes upon binding of its substrate. The receptor protein was attached to ECFP and an environmentally insensitive YFP derivative at opposite ends. Fluorescence resonance energy transfer changes were specifically observed after addition of arginine and to a lesser extent ornithine. The recombinant sensor showed a concentration-dependent increase in the fluorescence ratio with an apparent in vitro affinity for arginine of approximately 2 mM. A mutation in the binding pocket lowered the affinity and decreased the specificity. When expressed in E. coli, an increase in the fluorescence ratio was specifically detected after exposure to arginine and ornithine. Transient expression of the sensor in plant cell protoplasts and stable expression in Arabidopsis roots revealed specific fluorescence changes upon addition of arginine. The analysis suggests that fluorescent amino acid sensors may be versatile tools for studying the in vivo dynamics of metabolism and compartmentalization in plants.

A biosensor for inorganic phosphate using a rhodamine-labeled phosphate binding protein

A novel biosensor for inorganic phosphate (Pi) has been developed based on the phosphate binding protein of Escherichia coli. Two cysteine mutations were introduced and labeled with 6-iodoacetamidotetramethylrhodamine. When physically close to each other and correctly oriented, two rhodamine dyes interact to form a noncovalent dimer. In this state, they have little or no fluorescence, unlike the high fluorescence intensity of monomeric rhodamine. The labeling sites were so placed that the distance and orientation between the rhodamines change as a consequence of the conformational change associated with Pi binding. This movement alters the extent of interaction between the dyes. The best mutant of those tested (A17C, A197C) gives rise on average to approximately 18-fold increase in fluorescence intensity as Pi binds. The kinetics of interaction with Pi were measured at 10 degrees C. Under these conditions, the fluorescence increase associated with Pi binding has a maximum rate of 267 s-1. The Pi dissociation rate is 6.6 s-1, and the dissociation constant is 70 nM. An application of the sensor is demonstrated for measuring ATP hydrolysis in real time as a helicase moves along DNA. Advantages of the new sensor are discussed, both in terms of the use of a rhodamine fluorophore and the potential of this double labeling strategy.

Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy

Computational design of proteins with altered ligand specificity is an emerging method for the creation of new biosensing systems. In this work, we investigated the outcome of site-directed mutagenesis on the Escherichia coli ribose binding protein (RBP), which is frequently used as a design scaffold for computational searches. A ribose biosensor was first constructed whereby an environmentally sensitive fluorescent probe was covalently attached to RBP at position S265C. This protein conjugate displayed a 54% decrease in emission intensity upon the addition of saturating ribose concentrations and exhibited an apparent dissociation constant (K(d) ) of 3.4 microM. Site-directed mutants within the RBP binding pocket were created and examined for ribose binding ability and overall structural stability. Because as many as 12 mutations are needed to alter ligand specificity in RBP, we measured the effect of single and multiple alanine mutations on stability and signal transduction potential of the ribose biosensor. Single alanine mutations had significant impact on both stability and signaling. Mutations of N190A and F214A each produced melting temperatures >8 degrees C below those observed for the wild-type protein. Residue Q235, located in the hinge region of RBP, appeared to be a hot spot for global protein stability as well. Additional single alanine mutations demonstrated as much as 200-fold increase in apparent K(d) but retained overall protein stability. The data collected from this study may be incorporated into design algorithms to help create more stable biosensors and optimize signal transduction properties for a variety of important analytes.

Glutamine-Binding Protein from Escherichia coli Specifically Binds a Wheat Gliadin Peptide Allowing the Design of a New Porous Silicon-Based Optical Biosensor

In this work, the binding of the recombinant glutamine-binding protein (GlnBP) from Escherichia coli to gliadin peptides, toxic for celiac patients, was investigated by mass spectrometry experiments and optical techniques. Mass spectrometry experiments demonstrated that GlnBP binds the following amino acid sequence: XXQPQPQQQQQQQQQQQQL, present only into the toxic prolamines. The binding of GlnBP to gliadin suggested us to design a new optical biosensor based on nanostructured porous silicon (PSi) for the detection of trace amounts of gliadin in food. The GlnBP, which acts as a molecular probe for the gliadin, was covalently linked to the surface of the PSi wafer by a proper passivation process. The GlnBP-gliadin interaction was revealed as a shift in wavelength of the fringes in the reflectivity spectrum of the PSi layer. The GlnBP, covalently bonded to the PSi chip, selectively recognized the toxic peptide. Finally, the sensor response to the protein concentration was measured in the range 2.0-40.0 microg/L and the sensitivity of the sensor was determined.

Porous silicon-based optical microsensor for the detection of l-glutamine

The molecular binding between the glutamine-binding protein (GlnBP) from Escherichia coli and L-glutamine (Gln) is optically transduced by means of a biosensor based on porous silicon nano-technology. The sensor operates by the measurement of the interferometric fringes in the reflectivity spectrum of a porous silicon Fabry-Perot layer. The binding event is revealed as a shift in wavelength of the fringes. Due to the hydrophobic interaction with the Si-H terminated surface of the porous silicon, the GlnBP protein, which acts as a molecular probe for Gln, penetrates and links into the pores of the porous silicon matrix. We can thus avoid any preliminary functionalization process of the porous layer surface, which is also prevented from oxidation, at least for few cycles of wet measurements. The binding of Gln to GlnBP has also been investigated at different concentration of GlnBP.

Binding of glutamine to glutamine-binding protein from Escherichia coli induces changes in protein structure and increases protein stability

Glutamine-binding protein (GlnBP) from Escherichia coli is a monomeric protein localized in the periplasmic space of the bacterium. It is responsible for the first step in the active transport of L-glutamine across the cytoplasmic membrane. The protein consists of two similar globular domains linked by two peptide hinges, and X-ray crystallographic data indicate that the two domains undergo large movements upon ligand binding. Fourier transform infrared spectroscopy (FTIR) was used to analyze the structure and thermal stability of the protein in detail. The data indicate that glutamine binding induces small changes in the secondary structure of the protein and that it renders the structure more thermostable and less flexible. Detailed analyses of IR spectra show a lower thermal sensitivity of alpha-helices than beta-sheets in the protein both in the absence and in the presence of glutamine. Generalized two-dimensional (2D) analyses of IR spectra reveal the same sequence of unfolding events in the protein in the absence and in the presence of glutamine, indicating that the amino acid does not affect the unfolding pathway of the protein. The data give new insight into the structural characteristics of GlnBP that are useful for both basic knowledge and biotechnological applications.

Fatty acid sensor for low-cost lifetime-assisted ratiometric sensing using a fluorescent fatty acid binding protein

Elevated free fatty acid (FA) levels lead to insulin resistance, hypertension, and microangiopathy, all of which are associated with type 2 diabetes. On the other hand, deficiencies of FA are indicative of certain neurodegenerative diseases, including autism. Thus, free FA levels are a diagnostic indicator for a variety of disorders. Here we describe the use of a commercially available FA binding protein labeled with acrylodan (ADIFAB), which we modified with a ruthenium metal-ligand complex with the intention of creating a low-cost FA sensor. The dual-labeled FA binding protein was used in lifetime-assisted ratiometric sensing (LARS) of oleic acid. For both steady-state and time-resolved luminescence decay experiments, the protein is responsive to oleic acid in the range of 0.02-4.7 microM. The emission at 432 nm, which is associated with the acrylodan occupying the FA binding site, decreases in intensity and red shifts to 505 nm on the addition of oleic acid. The intensities of the 505-nm peak due to the acrylodan displaced from the binding site by FA and of the 610-nm emission peak of ruthenium remained nearly unchanged. Fitting of the fluorescence decay data using the method of least squares revealed three emitting components with lifetimes of approximately 0.60, 4.00, and 370 ns. Fractional intensities of the emitting species indicate that changes in modulation between 2 and 10 MHz on binding of the protein with oleic acid are due mainly to the 4.00-ns component. The 0.60- and 370-ns components are assigned to acrylodan (505 nm) and ruthenium, respectively. Note that because ruthenium has a lifetime that is two orders of magnitude longer than that of acrylodan, the FA measurements were carried out at excitation frequencies lower than what can be done with acrylodan alone. Thus, low-cost instrumentation can be designed for a practical FA sensor without sacrificing the quality of measurements.

Writing 3D protein nanopatterns onto a silicon nanosponge

A three-dimensional protein nanopatterning method has been developed, based on local activation of porous silicon by electron beam. Proteins specifically bind to irradiated regions, and the depth of biomolecule nanopatterns can be controlled by varying the electron energy. This unique feature permits exploitation of the huge surface area of the sponge-like material, thus allowing concentration of a large amount of proteins on nanosized patterns. Moreover, the grafted biomolecules retain their full functionality, and the feasibility of a glucose sensor has been demonstrated.

Fluorescence properties of glutamine-binding protein from Escherichia coli and its complex with glutamine

In this work, the fluorescence of glutamine-binding protein (GlnBP) and its complex with glutamine (GlnBP/Gln) in native and unfolded forms was studied. The experimental data were interpreted on the basis of the results of the analysis of Trp and Tyr microenvironments taking into the account the data for GlnBP mutated forms Trp32Phe(Tyr) and Trp220Phe(Tyr), which have been obtained by Axelsen et al. (Biophys. J. 1991, 60, 650-659). This allowed us to explain the negligible contribution of Tyr residues to the bulk fluorescence of the native protein, the similarity of the fluorescence characteristics of GlnBP and GlnBP/Gln, and the uncommon effect of the excess of the fluorescence intensity at 365 nm (Trp emission) upon excitation at 297 nm respect to the excitation at 280 nm. The last effect is explained by the spectral dependence of the Trp 32 and Trp 220 contributions to the protein absorption. The protein Trp fluorescence dependence on the excitation wavelength must be taken into account for the evaluation of the Tyr residues contribution to the bulk fluorescence of protein, and in principle, it also may be used for the development of an approach for the decomposition of a multicomponent protein fluorescence spectrum.

Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor

We previously reported the construction of a family of reagentless fluorescent biosensor proteins by the structure-based design of conjugation sites for a single, environmentally sensitive small molecule dye, thus providing a mechanism for the transduction of ligand-induced conformational changes into a macroscopic fluorescence observable. Here we investigate the microscopic mechanisms that may be responsible for the macroscopic fluorescent changes in such Fluorescent Allosteric Signal Transduction (FAST) proteins. As case studies, we selected three individual cysteine mutations (F92C, D95C, and S233C) of Escherichia coli maltose binding protein (MBP) covalently labeled with a single small molecule fluorescent probe, N-((2-iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBD), each giving rise to a robust FAST protein with a distinct maltose-dependent fluorescence response. The fluorescence emission intensity, anisotropy, lifetime, and iodide-dependent fluorescence quenching were determined for each conjugate in the presence and absence of maltose. Structure-derived solvent accessible surface areas of the three FAST proteins are consistent with experimentally observed quenching data. The D95C protein exhibits the largest fluorescence change upon maltose binding. This mutant was selected for further characterization, and residues surrounding the fluorophore coupling site were mutagenized. Analysis of the resulting mutant FAST proteins suggests that specific hydrogen-bonding interactions between the fluorophore molecule and two tyrosine side-chains, Tyr171 and Tyr176, in the open state but not the closed, are responsible for the dramatic fluorescence response of this construct. Taken together these results provide insights that can be used in future design cycles to construct fluorescent biosensors that optimize signaling by engineering specific hydrogen bonds between a fluorophore and protein.

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.

Genetically engineered binding proteins as biosensors for fermentation and cell culture

The signal-transduction properties and the potential applications of two engineered binding proteins from E. coli were extensively studied. Both proteins have a single cysteine mutation in their polypeptide chains, which allow the introduction of an environmentally sensitive fluorophore: ANS for glucose-binding protein (GBP) and acrylodan for glutamine-binding protein (QBP). Both proteins respond to their ligands in the micromolar range. The proteins can be stored at 4 degrees C for at least 5 months. Apparent binding constant, protein concentration, and fluorophore are three major factors that affect the biosensor's responsive ranges. The binding of the ligand is quick and reversible in solution, but the unfavorable dissociation equilibrium and mass-transfer resistance for encapsulated proteins can delay the response to several minutes and the recovery to hours. Simulated results show that using dialysis tubing with a diameter of 1 mm or less is possible to reduce the recovery time to less than 30 minutes. The potential applications of GBP were studied in yeast fermentation and E. coli fermentations in three different scales: 150 mL, 5 mL, and 100 microL. The results were compared with an YSI 2700 Chemistry Analyzer. Although the latter could not give reliable results for the E. coli fermentations as the glucose concentration in LB medium is close to its lower detection limit, the glucose biosensor presented here was successfully applied to each situation. Glutamine-binding protein was tested in cell cultures of two different scales (100 mL and 100 microL) and the results were also compared with those obtained with YSI. Both QBP and YSI gave good results for the 100-mL cell culture, but the relatively large sample volume requirement of YSI (at least 5 microL) prevented it from being used in the 100-microL cell culture. Because of their small sample volume requirements (less than 1 microL) and high sensitivity, the assays described here might find wide applications in high-throughput bioprocessing.

Dual-Labeled Glucose Binding Protein for Ratiometric Measurements of Glucose

Highly sensitive glucose monitoring has potential applications in conditions where the glucose levels are below the detection limit of currently available technology. Examples include bioprocess monitoring of bacterial cultures and measurement of minute amounts of human interstitial fluid extracted by iontophoresis. Here we describe a ratiometric glucose sensor capable of measuring micromolar levels of glucose. This sensor is based on an E. coli glucose binding protein (GBP) labeled with two fluorophores. The L255C mutant of GBP was labeled with the environment-sensitive fluorophore, acrylodan, at the cysteine mutation and a long-lived metal ligand complex of ruthenium (ruthenium bis(2,2'-bipyridyl)-1, 10-phenanthroline-9-isothiocyanate) at the N-terminal. The acrylodan emission is quenched in the presence of glucose while the ruthenium emission remained constant, thereby serving as a reference. The sensitivity of the sensor is in the micromolar range (K(d) = 0.4-1.4 microM). Thus, it is possible to measure glucose concentrations at micromolar levels and higher (with dilution). Calculations of the fluorescence energy-transfer efficiency between acrylodan and ruthenium gave an approximate distance of 25 A between the two fluorophores, consistent with X-ray crystallographic data. The effect of temperature on glucose binding was measured and analyzed. Maximum signal changes and apparent binding constants increase with temperature. The enthalpy change for glucose binding as calculated from the apparent binding constants is approximately 43.1 kJ/mol. In addition to ratiometric measurements, the presence of the long-lived ruthenium metal ligand complex allows for low-cost modulation-based sensing.

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

The chemically and genetically remodeling of proteins with ligand binding specificities can be utilized to synthesize various protein-based microsensors for detecting single biomolecules. Here, we describe the construction and characterization of fluorophore-labeled glutamine binding proteins (QBP) and derivatives coupled to the independently designed hydrophobic polypeptide (E12) that can adhere onto solid surfaces via hydrophobic interactions. The single cysteine mutant (N160C QBP) modified with the three environmentally sensitive fluorescent dyes (IAANS, acrylodan, and IANBD ester) showed increased changes in fluorescence intensity induced by glutamine binding. The use of these conjugates as reagentless fluorescence sensors enables us to determine the glutamine concentrations (0.1-50 microM) in homogeneous solution. The fusion of N160C QBP with E12, (Gly4-Ser)n spacers (GSn), and IANBD resulted in the novel fluorescence sensing elements having an adhering capability to hydrophobic surfaces of unmodified microplates. In ELISA and fluorescence experiments for the microplates treated with a series of the conjugates, IANBD-labeled N160C QBP-GS1-E12 displayed the best reproducibility in adhesion onto the hydrophobic surfaces and the precise correlation between fluorescence changes and glutamine concentrations. The performance of the biosensor-attached microplate for glutamine titrations demonstrated that the hydrophobic interaction of E12 with solid surfaces is useful for effective immobilization of proteins that need specific conformational movements in recognizing particular biomolecules. Therefore, the technique using E12 as a surface-linking domain for protein adhesion onto unmodified substrates could be applied effectively to prepare microplates/arrays for a wide variety of high-throughput assays on chemical and biological samples.

Reagentless optical sensing of glutamine using a dual-emitting glutamine-binding protein

Glutamine is a major source of nitrogen and carbon in cell culture media. Thus, glutamine monitoring is important in bioprocess control. Here we report a reagentless fluorescence sensing for glutamine based on the Escherichia coli glutamine-binding protein (GlnBP) that is sensitive in the submicromolar ranges. The S179C variant of GlnBP was labeled at the -SH and N-terminal positions with acrylodan and ruthenium bis-(2,2'-bipyridyl)-1,10-phenanthroline-9-isothiocyanate, respectively. The acrylodan emission is quenched in the presence of glutamine while the ruthenium acts as a nonresponsive long-lived reference. The apparent binding constant, K'(d), of 0.72 microM was calculated from the ratio of emission intensities of acrylodan and ruthenium (I(515)/I(610)). The presence of the long-lived ruthenium allowed for modulation sensing at lower frequencies (1-10 MHz) approaching an accuracy of +/-0.02 microM glutamine. Dual-frequency ratiometric sensing was also demonstrated. Finally, the extraordinary sensitivity of GlnBP allows for dilution of the sample, thereby eliminating the effects of background fluorescence from the culture media.

Construction of a fluorescent biosensor family

Bacterial periplasmic binding proteins (bPBPs) are specific for a wide variety of small molecule ligands. bPBPs undergo a large, ligand-mediated conformational change that can be linked to reporter functions to monitor ligand concentrations. This mechanism provides the basis of a general system for engineering families of reagentless biosensors that share a common physical signal transduction functionality and detect many different analytes. We demonstrate the facility of designing optical biosensors based on fluorophore conjugates using 8 environmentally sensitive fluorophores and 11 bPBPs specific for diverse ligands, including sugars, amino acids, anions, cations, and dipeptides. Construction of reagentless fluorescent biosensors relies on identification of sites that undergo a local conformational change in concert with the global, ligand-mediated hinge-bending motion. Construction of cysteine mutations at these locations then permits site-specific coupling of environmentally sensitive fluorophores that report ligand binding as changes in fluorescence intensity. For 10 of the bPBPs presented in this study, the three-dimensional receptor structure was used to predict the location of reporter sites. In one case, a bPBP sensor specific for glutamic and aspartic acid was designed starting from genome sequence information and illustrates the potential for discovering novel binding functions in the microbial genosphere using bioinformatics.

Bioprocess monitoring

Electrochemical sensors for pH and dissolved oxygen remain the most commonly used in bioprocess monitoring, but continued research has resulted in improved optical sensors. Optical sensors for dissolved oxygen and dissolved carbon dioxide are now commercially available. Advances in optics and electronics are further driving down the costs of these sensors. In the near future, bioprocess optimization will change paradigms as massively parallel, fully instrumented bioreactors become available and high-throughput bioprocessing becomes a reality.