US 20080166747 A1
Biosensors are made by attaching covalently or non-covalently at least one reporter group to one or more specific positions of a bacterial periplasmic binding protein (bPBP). Upon binding of ligand to the biosensor, there is a change in the signal transduced by the reporter group.
1. A biosensor for ligand, which comprises a glucose binding protein (GBP) and at least one reporter group attached at position 183 of said GBP, wherein binding of glucose in a glucose-binding pocket of said biosensor causes a change in signaling by said reporter group.
2. The biosensor according to
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16. A method of detecting presence or absence of glucose in a sample, which comprises: contacting a biosensor according to
17. A method of quantitating amount or concentration of glucose in a sample, which comprises: contacting a biosensor according to
18. A method of assaying for glucose in a sample, which comprises:
(a) contacting a biosensor according to
(b) measuring a ratiometric change (ΔR) for the signal transduced by said reporter group; and
(c) at least detecting or quantitating ligand present in said sample.
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This application claims the benefit of provisional Appln. No. 60/418,359, filed Oct. 16, 2002.
The U.S. Government has certain rights in this invention as provided for by the terms of NIH-RO1-GM49871 and ONR-N00014-98-1-0110.
The present invention relates to biosensors and to methods of making and using same.
Biosensors are analytical tools that can be used to measure the presence of a single molecular species in a complex mixture by combining the exquisite molecular recognition properties of biological macromolecules with signal transduction mechanisms that couple ligand binding to readily detectable physical changes (Hall, Biosenisors, Prentice-Hall, Englewood Cliffs, N.J.; Scheller et al., Curr. Op. Biotech. 12:35-40, 2001). Ideally, a biosensor is reagentless and, in contrast to enzyme-based assays or competitive immunoassays, does not change composition as a consequence of making the measurement (Hellinga & Marvin, Trends Biotech. 16:183-189, 1998). Most biosensors combine a naturally occurring macromolecule such as an enzyme or an antibody, with the identification of a suitable physical signal particular to the molecule in question, and the construction of a detector specific to that system (Meadows, Adv. Drug Deliv. Rev. 21:177-189, 1996). Recently, molecular engineering techniques have been explored to develop macromolecules that combine a wide range of binding specificities and affinities with a common signal transduction mechanism, to construct a generic detection system for many different analytes (Hellinga & Marvin, Trends Biotech. 16:183-189, 1998).
Escherichia coli periplasmic binding proteins are members of a protein superfamily (bacterial periplasmic binding proteins, bPBPs) (Tam & Saier, Microbiol. Rev. 57:320-346, 1993) that has been shown to be well suited for the engineering of biosensors (U.S. Pat. No. 6,277,627). These proteins comprise two domains linked by a hinge region (Quiocho & Ledvina, Molec. Microbiol. 20:17-25, 1996). The ligand-binding site is located at the interface between the two domains. The proteins typically adopt two conformations: a ligand-free open form, and a ligand-bound closed form, which interconvert via a hinge-bending mechanism upon ligand binding. This global, ligand-mediated conformational change has been exploited to couple ligand binding to changes in fluorescence intensity by positioning single, environmentally sensitive fluorophores in locations that undergo local conformational changes in concert with the global change (Brune et al., Biochemistry 33:8262-8271, 1994; Gilardi et al., Prot. Eng. 10:479-486, 1997; Gilardi et al., Anal. Chem. 66:3840-3847, 1994; Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997, Marvin and Hellinga, J. Am. Chem. Soc. 120:7-11, 1998; Tolosa et al., Anal. Biochem. 267:114-120, 1999; Dattelbaum & Lakowicz, Anal. Biochem. 291:89-95, 2001; Marvin & Hellinga, Proc. Natl. Acad. Sci. USA 98:4955-4960, 2001; Salins et al., Anal. Biochem. 294:19-26, 2001). Conformational coupling mechanisms can also be devised to alter the flow of current between the surface of an electrode derivatized with the engineered bPBP containing a covalently attached redox cofactor (Benson et al., Science 293: 1641-1644, 2001).
The present invention provides a method of utilizing bPBPs to generate biosensors for a variety of chemical classes including sugars, amino acids, dipeptides, cations, and anions. These biosensors have widespread utility including in clinical, industrial, and environmental settings.
The present invention relates to biosensors, making them from mutant or wildtype members of the bacterial periplasmic binding protein (bPBP) superfamily, and using them to assay for (i.e., detect and/or quantitate) ligand. The tertiary structure of bPBPs is comprised of two domains linked by a hinge region with a ligand-binding pocket located at an interface between the two domains. They typically adopt two conformations: a ligand-free open form and a ligand-bound closed form, which interconvert via a hinge-bending mechanism which depends on whether ligand is bound or not at the site. Biosensors are made by covalently or non-covalently attaching at least one reporter group to one or more specific positions of a bPBP. Upon binding of ligand to the biosensor, there is a change in the signal transduced by the reporter group which can be analyzed by assessing any of its observable properties (e.g., optical or electrochemical properties). Biosensors are classified according to the relationship between the attachment site of the reporter group and the binding site(s) of the ligand (i.e., allosteric, endosteric, or peristeric) or distance between those sites (i.e., distal or proximal).
In accordance with the invention, the event of ligand binding to biosensor changes the local environment of the position-specific attached reporter group. The signal of the reporter group may be generated by one or more fluorophores and/or redox cofactors. The biosensor may be operated under physiological conditions without additional reagents.
Objects and advantages of the present invention will be clear from the description that follows.
The present invention relates to biosensors constructed using engineered bPBPs, for example, E. coli bPBPs. In accordance with the invention, conjugates are constructed that can be used to monitor binding of ligands to bPBPs. Conjugates can be produced by introducing mutations into a bPBP at one or more specific positions in the protein structure where covalently attached reporter groups (e.g., fluorophores or redox cofactors) respond to a conformational change of the bPBP which occurs upon ligand binding. Other methods for covalently or non-covalently attaching at least one reporter group to one or more amino acid residue positions in the primary amino acid sequence of a mutant or wildtype bPBP include: addition or substitution of any activatable crosslinkers, use of designer or non-natural tRNAs, introduction of coordination sites, etc.
The universality of the engineered conformational coupling mechanism in bPBPs is disclosed herein. As described in the Example that follows, ten bPBPs of known structure have been used, and eight different environmentally sensitive fluorophores have been introduced at a variety of locations predicted to link local conformational changes to ligand-mediated hinge-bending motion. Bioinformatics techniques can be used to predict the location of linked sites in bPBPs the structures of which are not known, thereby making it possible to use the large number of paralogs and homologs that have recently been identified in this family by genomic sequencing studies (Blattner et al., Science 277:1453-1474, 1997; Quentin et al., J. Mol. Biol. 287:467-484, 1999). Together with the opportunities of structure-based redesign of ligand-binding specificity (Hellinga & Richards, J. Mol. Biol. 222:763-785, 1991; Marvin & Hellinga, Proc. Natl. Acad. Sci. USA 98:4955-4960, 2001), the Example provided below demonstrates the vast potential of the bPBP superfamily as the basis for a system of biosensors suited to a broad range of applications.
Furthermore, the ligand-binding pocket may be engineered to bind ligands which are not bound by the wild-type bPBP. The ligand-binding site is located at the interface between the bPBP's two domains. Mutating amino acid residues at that interface which are near (i.e., in or around) the binding site of wild-type bPBP may generate new contacts with ligand (e.g., Zn++ for MBP) and destroy or alter binding with cognate ligand (e.g., maltose for MBP). This can be used to change the specificity of the ligand-binding pocket. For example, maltose binding protein has been mutated to specifically bind to noncognate ligand: e.g., metal Zn++ ion, trinitrotoluene, L-lactate, and serotonin (Marvin & Hellinga, Proc. Natl. Acad. Sci. USA 98:4955-4960, 2001; Looger et al., Nature 423:185-190, 2003; Dwyer et al., Proc. Natl. Acad. Sci. USA 100:11255-11260, 2003). Thus, biosensors which bind noncognate ligand can be made by mutating amino acid residues at the interface of the two bPBP domains to generate a new ligand-binding pocket; ligand bound by such biosensors may not bind to wild-type bPBP.
Other mutations in the bPBP may be made to affect function of the biosensor: e.g., mutations may increase or decrease binding affinity or specificity; enhance or reduce signal transduction; add a new functionality by fusion with another carbohydrate, lipid, or protein domain; improve thermostability or thermolability; introduce a catalytic activity; shorten or lengthen operational life; widen or narrow the conditions for operation; or any combination thereof. Preferred is mutating amino acid residues at positions of the bPBP where a reporting group is not attached (e.g., at least one missense mutation which is not a cysteine conjugated through a thiol bond to a fluorophore).
In one embodiment, the present invention relates to a method of constructing a reagentless fluorescent biosensor. The method comprises identifying sites on a bPBP that undergo a local conformational change in concert with a ligand-mediated hinge-bending motion. Cysteine residues can be introduced at one or more such sites and a fluorophore coupled thereto so that fluorescence intensity of the fluorophore changes upon ligand binding.
bPBPs suitable for use in the present method can be selected or designed. The bPBP superfamily is well suited for the redesign of ligand-binding specificities either by computational methods or by other means or both based on the ligand to be detected (see, for example, analytes referenced in Table 1). Sites on the bPBP appropriate for attachment of one or more reporters (e.g., fluorophores or redox cofactors) include allosteric sites, peristeric sites, and endosteric sites (a reporter can also be present at a non-signaling site for use, for example, as a reference). In the case of an allosteric site, the reporter (e.g., fluorophore) can be placed at one or more locations distant from the ligand-binding site (i.e., distal from the ligand-binding pocket) that undergo local conformational changes upon ligand binding. In the case of a peristeric site, the reporter (e.g., fluorophore) can be positioned on the “rim” of the binding site but not such that it directly interacts with the ligand. With an endosteric site, the reporter (e.g., fluorophore) can be present in the binding site so that it interacts directly with the ligand. The latter two examples show attachment proximal to the ligand-binding pocket.
Allosteric, peristeric, and endosteric sites can be designed in at least two different ways, as detailed in the Example that follows. Generally, a structure-based design approach can be used in which the structures of the open and closed states (for allosteric designs) or the closed state only (for peristeric and endosteric designs) are examined. Alternatively, a sequence-based design approach can be used wherein homology relationships can be exploited to predict the location of cysteine mutations in proteins the three-dimensional structures of which have not been determined, provided that such mutations have been characterized in proteins of known structure.
As indicated above, reporters suitable for use in the invention include, but are not limited to, fluorophores and redox cofactors. In the case of fluorophores, the choice is dependent, at least in part, on the nature of the location within the particular protein. While one fluorophore may function better in a certain location than another, one skilled in the art can readily select the preferred fluorophore for a particular application (see, for example, U.S. Pat. No. 6,277,627). In the Example that follows, eight different fluorophores are used in the design of fluorescent sensors for:
Redox reporters for use in the invention can be a redox-active metal center or a redox-active organic molecule. It can be a natural organic cofactor such as NAD, NADP, FAD or a natural metal center such as Blue Copper, iron-sulfur clusters, or heme, or a synthetic center such as an organometallic compound such as a ruthenium complex, organic ligand such as a quinone, or an engineered metal center introduced into the protein or engineered organic cofactor binding site. Cofactor-binding sites can be engineered using rational design or directed evolution techniques. The redox reporter can be covalently or non-covalently attached to the protein, either by site-specific or adventitious interactions between the cofactor and protein. It can be intrinsic to the protein such as a metal center (natural or engineered) or natural organic (NAD, NADP, FAD) or organometallic cofactor (heme), or extrinsic (such as a covalently conjugated, synthetic organometallic cluster). The redox reporter can be, for example, bound (e.g., covalently) at a position where the amino acid residue is on the protein's surface.
The redox reporter can be a metal-containing group (e.g., a transition metal-containing group) that is capable of reversibly or semi-reversibly transferring one or more electrons. A number of possible transition metal-containing reporter groups can be used. Advantageously, the reporter group has a redox potential in the potential window below that subject to interference by molecular oxygen and has a functional group suitable for covalent conjugation to the protein (e.g., thiol-reactive functionalities such as maleimides or iodoacetamide for coupling to unique cysteine residues in the protein). The metal of the reporter group should be substitutionally inert in either reduced or oxidized state (i.e., advantageously, exogenous groups do not form adventitious bonds with the reporter group). The reporter group can be capable of undergoing an amperometric or potentiometric change in response to ligand binding. In a preferred embodiment, the reporter group is water soluble, is capable of site-specific coupling to a protein (e.g., via a thiol-reactive functional group on the reporter group that reacts with a unique cysteine in the protein), and undergoes a potentiometric response upon ligand binding. Suitable transition metals for use in the invention include, but are not limited to, copper (Cu), cobalt (Co), palladium (Pd), iron (Fe), ruthenium (Ru), rhodium (Rh), osmium (Os), rhenium (Re), platinum (Pt), scandium (Sc), titanium (Ti), vanadium (V), chromium (Cr), manganese (Mn), nickel (Ni), molybdenum (Mo), technetium (Tc), tungsten (W), and iridium (Ir). That is, the first series of transition metals, the platinum metals (Ru, Rh, Pd, Os, Ir, and Pt), along with Fe, Re, W, Mo, and Tc, are preferred. Particularly preferred are metals that do not change the number of coordination sites upon a change in oxidation state, including ruthenium, osmium, iron, platinum and palladium, with ruthenium being especially preferred.
The reporter group can be present in the biosensor as a covalent conjugate with the protein or it can be a metal center that forms part of the protein matrix (for instance, a redox center such as iron-sulfur clusters, heme, Blue copper, the electrochemical properties of which are sensitive to its local environment). Alternatively, the reporter group can be present as a fusion between the protein and a metal binding domain (for instance, a small redox-active protein such as a cytochrome). Preferably, the reporter group is covalently conjugated to the protein via a maleimide functional group bound to a cysteine (thiol) on the protein. In any case, the reporter group is attached to the protein so that it is located between the protein and the electrode.
Engineered proteins of the invention can be produced by site-specifically introducing a reporter group(s) by total synthesis, semi-synthesis, or gene fusions (see, for example, Adams et al., Nature 39:694-697, 1991; Brune et al., Biochemistry 33:8262-8271, 1994; Gilardi et al., Anal. Chem. 66:3840-3847, 1994; Godwin et al., J. Am. Chem. Soc. 118:6514-6515, 1996; Marvin et al., Proc. Natl. Acad. Sci. U.S.A. 94:4366-4371, 1997; Post et al., J. Biol. Chem. 269:12880-12887, 1994; Romoser, J. Biol. Chem. 272:13270-13274, 1997; Thompson et al., J. Biomed. Op. 1:131-137, 1996; Walkup et al., J. Am. Chem. Soc. 119:5445-5450, 1997).
Assays for ligand may be performed with the biosensor. A sample is contacted with the biosensor under appropriate assay conditions. Ligand present in the sample, if any, may be detected by binding to the biosensor and measuring the signal transduced by ligand-bound biosensor in the assay. For detection purposes, binding does not need to be quantitative because a simple determination of whether the ligand is present or absent (within detection limits) needs to be performed. Otherwise, comparison to a series of control samples (e.g., known quantities of ligand) may be required to quantitate the amount or concentration of ligand in the sample. Given the volume of the sample, the amount (i.e., mass) of ligand and the concentration of ligand are interconvertible. A blank sample containing no ligand may be used to determine background signal. Standards may be used to construct a standard curve (e.g., hyperbolic) used to quantitate unknown samples. Although homogeneous assay formats (i.e., those requiring no separation of bound and non-bound ligand) are preferred, separation in a heterogeneous assay format may be required if substances which significantly interfere with signal transduction and/or measurement are present in the sample. Signal transduction preferably does not require the addition of exotic reagents so assays of body fluids may be performed with minimal sample preparation and under physiological conditions. They may even be performed in vivo if the biosensor is adapted to an implantable medical device. Alternatively, a biosensor in contact with the skin may assay interstitial fluid or perspiration. Lavage may be used to sample mucosal tissues.
The sample can be obtained in a laboratory setting (e.g., clinic or research institution); from an environmental source (e.g., air, aquafers and other bodies of water, animal or plant products grown on the land, soil); from an industrial source (e.g., the food, biopharmaceutical, chemical, or other manufacturing industries). The analyte to be assayed is identical to the ligand, comprised of multiple copies of the ligand, chemically related to the ligand such that it is identified by a change in signal transduction (e.g., a related chemical structure is more strongly or more weakly bound by the biosensor as compared to its “correct” ligand), or any combination thereof. The change in signal transduction may be correlated to the change in chemical structure such that the non-identical analyte is identified (see below description of integrative assays). Examples of ligands which may be detected or quantitated include: amino acids; carbohydrates; bioactive solid and gaseous compounds which are soluble in an aqueous sample; contraband or controlled substances (i.e., substances which are illegal to use or possess, or which are highly regulated); environmental pollutants (e.g., phosphates, sulfates); explosives (e.g., TNT); food contaminants and byproducts (e.g., carcinogens, plant toxins, teratogens); lipids; metal ions (e.g., divalent cations, ferric ions); microbial toxins (e.g., toxic products of viruses, bacteria, or protozoa); neurotransmitters (e.g., serotonin); nucleosides or nucleotides (e.g., NAD, NADP, FAD); peptides or steroids (e.g., growth factors, hormones, morphogenic or developmental signals); and therapeutic drugs. Objects (e.g., baggage, mail, other containers); people or vehicles passing through a checkpoint; and borders or secure areas may be inspected for biological agents, contraband, explosives, poisons, and toxins in security or military applications.
One or more biosensors may be covalently or noncovalently attached to a solid or porous substrate. The substrate may be flat and planar (e.g., filter membrane, glass slide, semiconductor chip); cylindrical (e.g., optical fiber, plastic rod); spherical (e.g., crosslinked polymer or glass bead); or formed as a container (e.g., cell or cuvette, multiwell plate). The substrate may be fabricated for analysis by instruments which measure the signal transduced by the reporter group (e.g., microscope, photometer, spectrometer). Individual biosensors may be coded by an attached marker (e.g., bar code, radio frequency or RFID, or biopolymer) which can be decoded by a reader (e.g., scanner of light-and-dark patterns, radio receiver, specific binding probe or automated sequencer) or separated by a sorter in accordance with their marker. The code identifying each biosensor may be used in parallel analysis by rapidly assaying a sample for a plurality of ligands. Multiple biosensors with different ligand-binding specificities are used in the same assay to detect and/or quantitate multiple ligands at the same time. Alternatively, attaching different biosensors at particular spots on the substrate may be used to identify their ligand-binding specificities by where the signals are being produced. Signals may be authenticated by repeating the assay, using multiple biosensors with the same specificity for redundant assays, or correlating the results from multiple biosensors with overlapping specificities for integrative assays. In the latter, particular reactivity patterns of the biosensors are correlated with the identity of the analyte bound by them. Analytes that are more closely related in their chemical structure to the ligand will bind more strongly to the cognate biosensor. Signals from a plurality of biosensors with overlapping, known ligand-binding specificities are integrated to deduce the identity of the analyte.
The invention relates, in further embodiments, to biosensors constructed using the above-described methods and to the use thereof in analyte detection in, for example, clinical, industrial, and environmental settings. Particular utilities are described in the specific Example that follows. Provided is a description of a number of sites that can be used for optical glucose sensors based on GBP (W183C conjugated to acrylodan has been used successfully in fiber-optic prototypes of a glucose sensor).
To the extent that specific biosensors constructed in accordance with the present approach may be present in the public domain (e.g., may be disclosed in Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997 or in U.S. Pat. No. 6,277,627), such biosensors are not within the scope of the present invention.
Certain aspects of the invention can be described in greater detail in the non-limiting Example that follows.
Molecular Cloning. PCR was used to amplify wild-type genes for bPBPs from genomic DNA of E. coli strain CSH100 (arabinose, dipeptide, histidine, ribose, sulfate, and glutamate/aspartate BP); strain W1485 (glucose and glutamine BP) and strain RU1012 (phosphate BP), or of H. influenzae strain Rd (Fe(III) BP). Amplified products were cloned into one of the protein expression vectors pAED4 (Doering, “Functional and structural studies of a small f-actin binding domain” in Ph.D. thesis, Massachusetts Institute of Technology, 1992); pKK223-3 (Brosius & Holy, Proc. Natl. Acad. Sci. USA 81:6929-6933, 1984); or pET vectors (Studier et al., Meth. Enzymol. 185:60-89, 1990) (Novagen). N-terminal oligonucleotide primers were designed to clone only the processed periplasmic form, deleting the signal sequence. The C-terminal primer was designed to append the sequence Gly-Ser-Gly-(His)n or Gly-Ser-(His)n, where n=5, 6, or 10. Two tandem stop codons (TAATGA) follow the last His codon. Maltose BP mutants were made in and expressed from plasmid pMAL-c2X (New England BioLabs). E. coli strains XL1-BLUE (Stratagene) and DH5α (Hanahan, J. Mol. Biol. 166:557-580, 1983) were used for plasmid construction. Single amino acid substitutions were generated by overlapping PCR mutagenesis (Ho et al., Gene 77:51-59, 1989). All clones and mutations were confirmed by nucleotide sequencing. In the case of arabinose BP, the single cysteine in the wild type sequence was replaced by alanine to eliminate the possibility of reporter group conjugation to this thiol (Miller et al., J. Biol. Chem. 254:7521-7528, 1979). Additionally the sequence of Fe(III) BP was mutated by substitution of Glu57 with Asp to raise the Ki to a concentration range conveniently measured using Fe(III) citrate.
Protein Expression. Plasmids were transformed into E. coli strain BL21-DE3, grown in nutrient broth overnight at 37° C., then diluted 100-fold into fresh medium and grown further at 37° C. or 25° C. Expression was induced by the addition of isopropyl β-D-1-thiogalactopyranoside to 1 mM when the optical density of the culture at 600 nm reached 0.4. After 2 to 4 hours, cells were harvested by centrifugation, resuspended in 20 mM 3-morpholinopropanesulfonic acid (MOPS), 100 mM NaCl, pH 6.9 and stored frozen or lysed immediately for protein purification.
Protein Purification. Cells were lysed by sonication or by passage through a French pressure cell. The lysate was treated by adding Polymin P to 0.33% (w/v), chilling on ice for 15 min, then centrifuging to pellet cell debris. The supernatant was loaded on a Ni(II)-charged column of Chelating Sepharose™ Fast Flow (Amersham Pharmacia Biotech) equilibrated with 20 mM MOPS, 500 mM NaCl, 10 mM imidazole, pH 7.5. The column was washed with loading buffer, then with the same containing 60 mM imidazole, followed by the same with 100 mM imidazole. Finally, protein was eluted with loading buffer containing 400 mM imidazole, and was collected in fractions and assessed for purity by gel electrophoresis. All preparations were at least 95% pure by this criterion. Protein-containing fractions were dialyzed exhaustively against buffer (20 mM MOPS, 100 mM NaCl, pH 6.9, or 20 mM NaH2PO4, 100 mM NaCl, pH 6.9) or desalted by gel filtration to remove bound ligand.
Fluorophore conjugation to cysteine-substituted bPBPs. Thiol-reactive fluorophores obtained from Molecular Probes (Eugene, Oreg.) were 5-iodoacetamidofluorescein (fluorescein); N-(1-pyrene) iodoacetamide (pyrene); N,N′-dimethyl-N-(iodoacetyl)-N′-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylenediamide (NBD); N-((2-(iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBDE); and 6-acryloyl-2-dimethylaminonaphthalene (acrylodan). The styryl and naphthyl dyes JPW4039, JPW4042, and JPW4045 (
Depletion of sulfate and phosphate. Solutions of sulfate BP and phosphate BP and their buffers were treated to decrease the concentration of contaminating sulfate and phosphate, respectively. Sulfate BP buffer (20 mM Tris-HCl, pH 8.0) was passed through the chloride form of Dowex 1X2-100 strongly basic anion-exchange resin. Sulfate BP solutions were treated by dialysis against treated buffer; Dowex resin held in a separate dialysis tube was also included. Phosphate BP solutions and buffer (20 mM MOPS, 100 mM NaCl, pH 6.9) were depleted of phosphate by addition of 7-methylguanosine to 1 mM and dialyzed against bacterial nucleoside phosphorylase (1 unit ml−1) (Sigma-Aldrich) partitioned in a separate dialysis tube (Brune et al., Biochem. 33:8262-8271, 1994).
Fluorimetry. All measurements were conducted with an SLM Aminco-Bowman series 2 fluorimeter, with sample stirring at 25° C. Fluorescence emission spectra were acquired with excitation and emission slit widths of 4 and 8 nm, respectively. Photomultiplier tube potential was maintained between 400 and 800 volts. Protein concentrations were in the range of 50 to 1000 nM. Fluorophore-specific excitation was at the following approximate wavelengths: tryptophan, 290 nm; acrylodan, 390 nm; fluorescein, 485 nm; pyrene, 340 nm; NBD and NBDE, 490 nm; JPW4039, 485 nm; JPW4042, 470 nm; JPW4045, 470 nm.
To measure ligand binding affinity, ligand was serially added to 3 ml of bPBP at a concentration of 50 to 1000 nM, and emission intensities recorded. Corrections were made for dilution of the protein and for background signal from buffer. Binding curves were fit to binding isotherms using equation 3 or 4, as appropriate.
Fe(III) BP has a dissociation constant for Fe(III) on the order of 10−21 M (Adhikari et al., J. Biol. Chem. 270:25142-25149, 1995), hindering accurate fluorescence-based measurements of affinity at nanomolar protein concentrations. Hence we used Fe(III) citrate (logK˜10.25) (Martell and Smith, Critical Stability Constants, Plenum Press, New York, 1977) as the ligand in a competition assay.
Family of biosensors. A set of eleven bPBPs with widely varying ligand-binding specificities was selected for engineering biosensor function (Table 2). All were from E. coli except Fe(III) BP, which is from Haemophilis influenzae. Binding specificities and affinities of these proteins for their respective ligands have been characterized (references in Table 2). Three proteins bind monosaccharides (arabinose, glucose and ribose BP), one binds di- and trisaccharides of glucose (maltose BP), three bind amino acids (glutamate/aspartate, histidine, and glutamine BP), one binds di- and tripeptides (dipeptide BP), two bind oxyanions (phosphate and sulfate BP), and one binds a metal ion (Fe(III) BP). Most of these bPBPs bind at most two or three related ligands with high affinity (micromolar or better). For example, phosphate BP binds phosphate and arsenate but not other oxyanions (Luecke & Quiocho, Nature 347:402-406, 1990), while glucose BP binds glucose and galactose but not other monosaccharides (Anraku, J. Biol. Chem. 243:3116-3122, 1968). Dipeptide BP is an exception in that it binds a wide variety of di- and tripeptides (Smith et al., Microbiology 145:2891-2901, 1999). Measured ligand dissociation constants in these proteins are typically in the range of 0.1 to 1 μM. An exception is Fe(III) BP, where the Kd for Fe(III)(aq) is estimated to be 10−21 M in competition assays with Fe(III) chelates (Adhikari et al., J. Biol. Chem. 270:25142-25149, 1995).
For nine of the eleven proteins selected for this study crystal structures have been solved of the closed, ligand-bound state (Table 2). In the case of sulfate BP, the crystal structure of the E. coli protein has not been reported, so that of Salmonella typhimurium sulfate BP was adopted to model the E. coli protein. Sulfate BP from E. coli and S. typhimurium are 95% identical in amino acid sequence and hence likely to have highly similar structures, in analogy to histidine BP from these two organisms (Oh et al., J. Biol. Chem. 269:4135-4143, 1994; Yao et al., Biochemistry 33:4769-4779, 1994). Structures have been solved for the open unliganded state for six of the eleven proteins as well (Table 2).
Structure-based design of conformational coupling. Coupling between ligand binding and a change in the fluorescent signal of a covalently attached, environmentally sensitive fluorophore can be established if the local environment of the fluorophore changes as a result of formation of the complex and a linked conformational change. Two mechanisms can be distinguished to establish such structural linkage relationships. Direct linkage involves formation of a non-bonded contact between the bound ligand and the conjugated fluorophore. Indirect linkage involves changes in the local protein structure in the immediate vicinity of the attached fluorophore, and relies on ligand-mediated conformational changes such as the hinge-bending motion observed in the bPBPs.
Direct linkage relationships are readily designed by replacing a residue known to form a ligand contact with a cysteine to which the fluorophore is attached (“endosteric” attachment site). Indirect linkage relationships can be established in two ways. The most straightforward method relies on visual inspection of the ligand complex structure, and identifying residues that are located in the vicinity of the binding site, but do not interact directly with the ligand, and that are likely to be involved in conformational changes. In the case of the bPBPs, such are residues located at the perimeter of the inter-domain cleft that forms the ligand binding site. The environment of these “peristeric” sites changes significantly upon formation of the closed state. These are examples of positions which are proximal to the ligand-binding pocket. The second approach identifies sites in the protein structure that are located some distance away from the ligand-binding site (i.e., distal to the ligand-binding pocket), and undergo a local conformational change in concert with ligand binding. If the structures of both the open and closed states are known, then such “allosteric” sites can be identified using a computational method that analyzes the conformational change (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). Alternatively, once allosteric sites have been identified in one bPBP, modeling and structural homology arguments can be invoked to identify such sites in other bPBPs in which only one state has been characterized (Marvin & Hellinga, J. Am. Chem. Soc. 120:7-11, 1998). Table 3 summarizes the designs of all three classes of sites in each of the receptors used in this study. The locations of these sites in the eleven bPBPs are shown in
Sequence-based design of conformational coupling. The number of bPBPs of known sequence greatly exceeds the number for which structures have been solved or for which functions have been assigned by genetic or biochemical characterization. To exploit this reservoir of potential biosensors, coding sequences for bPBPs must be identified and their putative ligand-binding specificities must be established. The identification of bPBPs in microbial genomes relies on finding amino acid sequence homologies to particular clusters of the bPBP family (Tam & Saier, Microbiol. Rev. 57:320-346, 1993). Ligand-binding can then be determined by direct experimentation, or be inferred either by structural relationships to bPBPs of known function, or by establishing genetic linkage to other genes of known function (Pellegrini et al., Proc. Natl. Acad. Sci. USA 96:4285-4288, 1999). Subsequently sites within the homolog that undergo local conformational change, and to which reporter functions can be attached, must be identified. The selection of sites for attaching reporter functions relies on homology to bPBPs of known structure.
To illustrate these principles, a glutamate biosensor was constructed starting from genome sequence data only. The genome of E. coli K12 contains the locus ybeJ encoding a protein identified as a putative bPBP based on amino acid sequence homology with glutamine and histidine BPs (26% and 23% sequence identity; 41% and 43% sequence similarity, respectively) (Blattner et al., Science 277:1453-1474, 1997). The assignment of YBEJ as an amino-acid binding protein was strengthened by the presence of conserved residues found to be associated with binding to the α-amino and α-carboxylate groups of the ligand in all bPBP amino-acid binding proteins of known structure identified in E. coli (Table 4). Of additional interest is the presence of an arginine residue in YBEJ located at a position that in the other amino acid-binding proteins interacts directly with the side chain of the bound amino acid, suggesting that YBEJ binds an amino acid bearing a negatively charged side chain. Finally, ybeJ is located adjacent to three tandem genes (gltJ, gltK, gltL) postulated to be involved in the glutamate/aspartate transport system (Lum & Wallace, GenBank Accession Number U10981, 1995), suggesting that ybeJ encodes a glutamate/aspartate BP. Putative allosteric, endosteric, and peristeric sites were identified from a structure-based sequence alignment of YBEJ with glutamine BP and histidine BP (
Mutagenesis and protein production All the genes for the bPBPs used in this study were cloned from E. coli or H. influenzae genomic DNA using PCR. The leader peptide sequence that directs expression into the periplasm was identified by comparison to the known N-terminus of the protein, or, in the case of YBEJ, by homology to known leader sequences (von Heijne, Nucl. Acids Res. 14:4683-4690, 1986). The protein was produced by over-expression of the processed form in the cytoplasm with an initiation methionine placed just before the N-terminus of the processed protein, under the control of a strong inducible promoter in the pAED4 (Doering, “Functional and structural studies of a small f-actin binding domain” in Ph.D. thesis, Massachusetts Institute of Technology, 1992); pET-21a (Studier et al., Meth. Enzymol. 185:60-89, 1990) (Novagen); or pKK223-3 (Blattner et al., Science 277:1453-1474, 1997) plasmids. An oligohistidine tag was fused to the carboxy terminus of the cloned receptor to permit facile purification by immobilized metal affinity chromatography (Hochuli et al., J. Chromatogr. A 411:177-184, 1987). In all cases, the receptors expressed well (at least 50 mg of pure protein per liter of fermentation). The molecular masses estimated by gel electrophoresis corresponded to the predicted mass of the expressed reading frame.
Cysteine point mutations were introduced by the PCR overlap method (Ho et al., Gene 77:51-59, 1989). Mutant proteins typically expressed as well as the wild type protein. All cysteine substitutions in arabinose BP were constructed in the C64A background to prevent interference from this endogenous cysteine (Miller et al., J. Biol. Chem. 254:7521-7528, 1979). In the case of Fe(III) BP, all mutations were constructed in the E57D background. In the crystal structure of Fe(III) BP, this glutamate is coordinated to the iron (Bruns et al., Nat. Struct. Biol. 4:919-924, 1997). It was found that the E57D mutation weakens the affinity of Fe(III) BP for Fe(III) from approximately 1×10−21 (Adhikari et al., J. Biol. Chem. 270:25142-25149, 1995) to approximately 3×10−8, assuming a stability constant for the 1:1 Fe(III) citrate complex of logK=10.25 (Martell & Smith, Critical Stability Constants, Plenum Press, New York, 1977). This permitted straightforward determination of Fe(III) affinity by direct titration with Fe(III) citrate at nanomolar concentrations of Fe(III) BP.
Signal transduction by fluorescence. To report ligand binding by the set of eleven bPBPs, fluorescent reporter groups were attached to single cysteine thiols engineered into sites that were predicted to undergo binding-dependent conformational change. Eight thiol-reactive fluorophores were examined that were chosen on the basis of the sensitivity of their emission spectra to changes in environment and spanning a wide range of emission and excitation wavelengths (
Assessment of fluorescent biosensor function. Fluorescence emission spectra of bPBP-fluorophore conjugates were recorded in the absence and presence of saturating ligand concentrations. Spectral changes were characterized by four parameters: wavelength shift (the difference between the wavelengths of emission maximum in the unbound and ligand-saturated states), direction of intensity change (increase or decrease in intensity at the wavelengths of maximum emission in the two states), standard intensity change (ΔIstd), and standard ratiometric change (ΔR). ΔIstd is defined as the normalized intensity change relative to the average intensity, determined at the wavelength mid-point between the two emission maxima:
where λstd=(λmax, unbound+λmax, saturated)/2 and I1, I2 are the fluorescence intensities at λstd of each spectrum respectively (
where 0A1, ∞A2 are the areas in the absence of ligand, and ∞A1, ∞A2 the areas in the presence of saturating ligand. A computer program was used to enumerate ΔR for all possible pairs of wavelength bands in the two spectra, to identify the optimal sensing condition, defined as the maximum value of ΔR. Adjustable parameters of the algorithm, and their values used for ΔRmax quantities reported here, are: step size (2 nm), step width (10 nm), minimum integration area limit (fraction of total: 0.1), and maximum integration area limit (fraction of total: 1).
Analyte affinity measurements. 133 bPBP-fluorophore conjugates with ΔIstd>0.1 were used to determine ligand binding affinity by fluorimetric titration (Table 5). The emission wavelength monitored was that of maximum difference in intensity between the ligand-free and bound states. For each conjugate, fluorescence intensiometric observations were fit to a hyperbolic binding isotherm for a two-state model (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997):
where F is fluorescence at ligand concentration [S], Kd is the dissociation constant, and FF, FB are the fluorescence intensities of the ligand-free and ligand-saturated states, respectively. Examples of binding isotherms are shown in
where R is ratio A1/A2, RB=∞A1/∞A2, RF=0A1/0A1, and appKd is an apparent dissociation constant:
The success of the fluorescent biosensor design strategy was evaluated by determining the probability of encountering an effectively responding fluorescent conjugate, and assessing how the ligand-binding affinities are affected by the fluorophore conjugate.
Assessment of ligand-mediated changes in fluorescence. Summaries of wavelength shift, ΔIstd, and ΔRmax for all conjugates (n=320) are presented as histograms in
The two criteria of greatest utility for optical sensing are ΔIstd and ΔRmax. The collection of bPBP conjugates was categorized by class of steric site, fluorophore, and protein scaffold, then, for each category, quantified according to the fraction with ΔIstd>0.25 and with ΔRmax>1.25. The results (Tables 6 to 8) give an indication of the overall success rate for finding potentially useful fluorescent biosensor conjugates. For the collection of 320 conjugates, about 24% meet the criterion for ΔIstd and about 28% the criterion for ΔRmax.
There appears to be a correlation between signaling success rate and the sequence-related family, or cluster (Tam & Saier, Microbiol. Rev. 57:320-346, 1993), to which a scaffold belongs. The scaffolds having the highest success rates for ΔIstd and ΔRmax are arabinose BP, glucose BP, ribose BP, and phosphate BP (Table 6). The former three belong to cluster 2, that includes binding proteins for hexoses and pentoses, while phosphate BP, along with sulfate BP, belongs to cluster 6, that includes binding proteins for inorganic polyanions. The scaffolds having the lowest success rate were dipeptide BP (cluster 5, peptide and nickel binding) and the cluster 3 (polar amino-acid binding) proteins glutamine BP, histidine BP, and Glu/Asp BP.
Among the three classes of attachment sites the endosteric and allosteric sites have a higher chance of meeting the threshold criteria than peristeric sites (Table 7). Success rates in terms of ΔIstd varied according to the environmental sensitivity of the fluorophore, being highest with the styryl and naphthyl dyes JPW4039, JPW4042, and JPW4045. Similarly, higher success rates for ΔRmax were associated with JPW4045 and acrylodan (Table 8).
Assessment of changes in ligand-binding affinities. The range of dissociation constants, Kd, extracted from the binding curves for each ligand is shown in Table 9. Since there is a thermodynamic linkage between ligand binding and the interaction of the attached fluorophore with the protein, the fluorophore is expected to change the intrinsic ligand dissociation constant. The change in affinity imparted by the fluorophore is expected to be dependent on its location in the protein. The various conjugates exhibit a wide range of affinities (Table 9). The change in affinity, defined as log(mutKd/wtKd), was examined as a function of attachment site classification (endosteric, allosteric, or peristeric) among the 108 conjugates for which dissociation constants were measured and for which the dissociation constant of the unconjugated protein is known (Table 2). The results reveal that the three classes of site have different effects on affinity (
The effect on dissociation constants is determined not only by the attachment site, but also by the nature of the attached fluorophore, as illustrated for arabinose BP. Dissociation constants for arabinose of the five cysteine-substitution mutants (all with the C64A mutation), measured by tryptophan fluorescence, are 5.0 μM (F23C), 3.2 μM (L253C), 3.4 μM (D257C), 7.6 μM (L298C), and 1.6 μM (K301C). Thus the cysteine substitutions slightly perturbed affinity for arabinose (Kd of C64A mutant ˜2.2 μM). The largest dependence on the attached fluorophore was found for the L253C mutant, for which Kd values ranged from 0.7 μM (acrylodan) to 775 μM (NBD). Similarly, the K394C mutant of dipeptide BP has affinities for Gly-Leu dipeptide ranging from 6 nM (NBD) to 93 μM (fluorescein). Most mutants did not exhibit such a wide range of fluorophore-dependent ligand affinity. For example, five different fluorophores conjugated to ribose BP E192C have affinities for ribose ranging from 2.6 μM (NBD and JPW4039) to 15 μM (JPW4045).
Construction of a novel biosensor using sequence information. To demonstrate that designs are not limited to those bPBPs with known structure, cysteine mutations were introduced into a paralog predicted to code for a glutamate/aspartate BP, using histidine and glutamine BPs as the structures to guide locations for likely peristeric and allosteric sites. All the ten sites that were tried yielded conjugates that exhibited glutamate and aspartate-dependent changes in fluorescence. Several sites yielded good or excellent intensiometric or ratiometric sensors. Table 10 shows that the response is specific for both aspartate and glutamate, with 50- to 500-fold weaker affinity for glutamine and asparagine. Other amino acids and sugars did not elicit ligand-mediated changes in fluorescence.
Bioinformatics makes possible the discovery of new biochemical applications without direct experimentation. In the case of biosensors, individual bacterial genomes may encode scores of bPBPs that bind specific molecules to initiate transport or signal transduction (Blattner et al., Science 277:1453-1474, 1997; Quentin et al., J. Mol. Biol. 287:467-484, 1999). Few of these have been characterized, leaving a vast number untapped as scaffolds for potential biosensors. The feasibility of applying genomic information, combined with structural information from homologous proteins, to construct a biosensor of novel specificity has been demonstrated.
Previously, a glutamate/aspartate BP had been purified from E. coli (Barash & Halpern, Biochim. Biophys. Acta 386:168-180, 1975; Willis & Furlong, J. Biol. Chem. 250:2574-2580, 1975) and characterized. Several pieces of evidence suggest that YBEJ corresponds to this protein. First, glutamate/aspartate BP was isolated from periplasmic extracts, consistent with ybeJ encoding a protein with a putative periplasmic localization signal sequence. Second, the previously determined molecular mass of glutamate/aspartate BP of 32 kDa (Barash & Halpern, Biochim. Biophys. Acta 386:168-180, 1975) or 31 kDa (Willis & Furlong, J. Biol. Chem. 250:2574-2580, 1975) match the mass of 32.5 kDa predicted for the processed ybeJ product, and the mass of 30 kDa found by gel electrophoresis in the present study. Third, the amino acid compositions determined previously (Barash & Halpern, Biochim. Biophys. Acta 386:168-180, 1975; Willis & Furlong, J. Biol. Chem. 250:2574-2580, 1975) are similar to that predicted from the gene sequence, with some deviations due likely to inherent inaccuracy in analysis of protein acid hydrolyzates. Finally, the reported Kd values for glutamate (0.8 μM), aspartate (1.2 μM), as well as the relatively lower affinity for glutamine and asparagine (Willis & Furlong, J. Biol. Chem. 250:2574-2580, 1975) are similar to those determined here, and comparable to the Q123C-fluorescein conjugate (Table 10). Hence, ybeJ likely encodes the glutamate/aspartate BP previously characterized.
Effective sensor designs. The utility of a conjugate is determined by the absolute change in signal intensity, the ratiometric change, and the operating concentration range over which the sensor can respond accurately. Of the two observable parameters, ratiometric change is preferable to absolute intensities, since it is independent of probe concentration.
Although usable conjugates can be defined as having ΔIstd>0.25 and ΔRmax>1.25, “excellent” sensors can be defined as having ΔIstd>0.9 and ΔRmax>2.5. The magnitudes of the changes in the excellent sensors are likely to be sufficiently large to permit robust measurements in “real-world” applications in complex fluids such as blood. Based on these criteria there are only thirteen excellent absolute intensity-based sensors (4% of total), but 36 excellent ratiometric sensors (11% of total); there are seven conjugates that are both excellent absolute intensity and excellent ratiometric sensors (Table 5). With the exception of dipeptide BP, Fe(III) BP, and histidine BP, all the proteins have at least one excellent ratiometric and intensity-based conjugate. Glucose BP has the largest number of excellent conjugates. These conjugates all involve fluorophores known to be particularly environmentally sensitive (acrylodan, NBD, pyrene, and the styryl dyes). The incidence of excellent sensors is evenly distributed between allosteric and peristeric sites. All endosteric sites give rise to excellent sensors.
The dissociation constant of a conjugate determines the operating concentration range over which the sensor can respond accurately. The operating range guaranteed to give less than a 5% error spans concentrations that fall within five-fold of the Kd value (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). If the range required for accurate determination is wider than that span, then a composite biosensor can be constructed using receptors of varying affinities, as has been demonstrated for maltose BP (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). There are three factors affecting the dissociation constant: the nature of the conjugate, the choice of emission bands for a ratiometric sensor (eq. 2), and additional mutations. For particular applications, these three factors can be manipulated to construct an appropriate sensor.
Glucose sensor. Among the analytes applicable to clinical medicine, glucose is one of the most important, particularly with regard to diagnosing and treating diabetes. The normal range of glucose concentration in adult human serum is 4 to 6 mM (Burtis & Ashwood, Teitz Textbook of Clinical Chemistry, 2nd Ed. W.B. Saunders Co., Philadelphia, Pa., 1994). The acrylodan conjugate of the endosteric site W183C in glucose BP has an excellent ratiometric response (ΔRmax=5.57) and a dissociation constant of 5.98 mM, and is therefore a good candidate for detecting glucose fluctuations in the physiological range by ratiometry (
Other sensors for clinical chemistry. Amino acids are also commonly assayed in clinical tests as indicators of disease states. Histidine is an indicator of histidase deficiency (Taylor et al., Molec. Biol. Med. 8: 101-116, 1991). The best signaling histidine BP conjugate, V163C-JPW4042, has a Kd of 0.25 μM, below the normal range in serum of about 48 to 125 μM. However, with sample dilution this conjugate could function effectively. Alternatively the Kd can be adjusted by mutagenesis as was done for maltose BP (Marvin & Hellinga, Nat. Struct. Biol. 8:795-798, 2001) and Fe(III) BP with the E57D mutation. The neuroexcitatory amino acid glutamate has normal serum concentrations of 20 to 220 μM (Burtis & Ashwood, Teitz Textbook of Clinical Chemistry, 2nd Ed. W.B. Saunders Co., Philadelphia, Pa., 1994). The best-suited biosensor is glutamate/aspartate BP F126C-acrylodan, which has a Kd˜80 μM and ΔRmax=2.70. Glutamine is often measured in cerebrospinal fluid (Smith & Forman, Clin. Lab. Sci. 7:32-38, 1994) in which its normal range is 120 to 360 μM, considerably higher than the Kd (˜1.4 μM) of the best-signaling glutamine BP conjugate, Y163C-acrylodan. This biosensor can be used for such a purpose by mutagenesis to adjust the Kd, or by sample dilution.
Phosphate concentrations in serum and urine are clinically relevant (Burkhardt et al., Am. J. Clin. Pathol. 72:326-329, 1979). Several phosphate BP conjugates signal well, the best being S39C-JPW4045, and their Kd values are all less than 2 μM. Inorganic phosphate in serum is typically 1 to 3 mM (Burtis & Ashwood, Teitz Textbook of Clinical Chemistry, 2nd Ed. W.B. Saunders Co., Philadelphia, Pa. 1994), requiring adjustment of the Kd or sample dilution for accurate measurements with these sensors.
Maltose concentration is relevant to a deficiency in acid maltase, with the normal plasma concentration about 2 μM (Rozaklis et al., Clin. Chem. 48:131-139, 2002). The best maltose sensors in the present work are maltose BP conjugates S233C-JPW4042 (ΔRmax=4.0) and S233C-JPW4045 (ΔRmax=3.9), both with similar affinities (Kd˜400 μM). Fluorescent conjugates of maltose BP mutants having affinities in the 2 μM range have been described by Marvin et al. (Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997).
Industrial and environmental applications. bPBP conjugates can function as sensors for industrial and environmental analytes. Arabinose is relevant to improving the efficiency of ethanol production from corn (Deanda et al., Appl. Environ. Microbiol. 62:4465-4470, 1996). Of the arabinose BP conjugates, the best signalers are K301C-NBD (Kd˜31 μM, ΔRmax=3.2) and L253C-fluorescein, (Kd˜48 μM, ΔRmax=2.7). Ribose concentration, assayed in foods and beverages (AOAC, Official Methods of Analysis of AOAC International, 16th Ed. AOAC International, Arlington, Va., 1995), can be measured by ribose BP conjugates T135C-acrylodan (Kd˜0.4 mM, ΔRmax=6.3) and A234C-JPW4045 (Kd˜3.8 μM, ΔRmax=4.1). Ratiometric sensing of ribose using a single ribose BP derivative is illustrated by the T135C-acrylodan conjugate (
All documents cited above are hereby incorporated in their entirety by reference. Also incorporated by reference for their disclosure of electronic devices containing bioelectronic sensors are U.S. application Ser. No. 10/229,286 (published as US 2003/0129622) and Int'l Appln. No. PCT/US02/27279 (WO 03/021247).