# Patent

## Title
Development of sensitive FRET sensors and methods of using the same

## Abstract

Intramolecular biosensors are disclosed, including PBP-based biosensors, comprising a ligand binding domain fused to donor and fluorescent moieties that permit detection and measurement of Fluorescence Resonance Energy Transfer upon binding ligand. At least one of the donor and fluorescent moieties may be internally fused to the biosensor such that both ends of the internally fused fluorophore are fixed. In addition, methods of improving the sensitivity of terminally fused biosensors are provided. The biosensors of the invention are useful for the detection and quantification of ligands in vivo and in culture.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
The present application is a U.S. National Phase Application of International Application No. PCT/US2005/036957, filed Oct. 14, 2005, which claims the benefit of U.S. Provisional application 60/618,179, filed Oct. 14, 2004, U.S. Provisional application 60/643,576, filed Jan. 14, 2005, U.S. Provisional application 60/654,447, filed Feb. 22, 2005, and U.S. Provisional application 60/658,141, filed Mar. 4, 2005, which are herein incorporated by reference in their entireties.
This application is also related to provisional application Ser. No. 60/658,142, provisional application Ser. No. 60/657,702, PCT application no. PCT/US2005/036955 PCT application no. PCT/US2005/036953, and PCT application no. PCT/US2005/036951, which are herein incorporated by reference in their entireties.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was funded through two grants, including an NIH subcontract from Duke University (Subcontract No. SPSID 126632) and a Human Frontier Science Program grant (Contract No. RGP0041/2004C). This invention was also funded by DOE Grant No. DE-FG02-04ER15542 and by NIH Grant No. 1 R33 DK070272. Accordingly the U.S. Government has certain rights to this invention.


FIELD OF INVENTION
The invention relates generally to the field of molecular biology and metabolomics. More specifically, the invention relates to biosensors and methods for measuring and detecting ligand binding using intramolecular fluorescence resonance energy transfer (FRET).
BACKGROUND OF INVENTION
All publications and patent applications herein are incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention.
The field of metabolomics centers on the metabolic and biochemical events associated with a cellular or biological system. Metabolomics seeks to depict the steady-state physiological state of a cell or organism as well as dynamic responses of a cell or organism to genetic and environmental modulation. Metabolomic tools permit the detection of disease states, the monitoring of disease progression and patient response to therapy, the classification of patients based on biochemical profiles and the identification of targets for drug design.
An ideal metabolomic tool reveals the concentration of a particular molecular species of interest in a physiological environment. It allows one to visualize how its concentration varies across an organ, tissue or cell. It permits the detection of metabolite levels and the changes in metabolite levels in response to environmental stimuli, and allows these changes to be monitored in real time. Using various such tools should permit multiple analytes to be measured simultaneously, even analytes of different structural and functional classes.
No currently available technology addresses all these issues in a satisfactory manner. Non-aqueous fractionation is static, invasive, has no cellular resolution and is sensitive to artifacts, while spectroscopic methods such as NMRi (nuclear magnetic resonance imaging) and PET (positron emission tomography) provide dynamic data, but poor spatial resolution. The development of genetically encoded molecular sensors, which transduce an interaction of the target molecule with a recognition element into a macroscopic observable format, via allosteric regulation of one or more signaling elements, may facilitate some of the goals.
The most common reporter element employed in molecular sensors is a sterically separated donor-acceptor FRET pair of fluorescent proteins (GFP spectral variants or otherwise) (Fehr et al., 2002, Proc. Natl. Acad. Sci USA 99: 9846-51), although single fluorescent proteins (Doi and Yanagawa, 1999, FEBS Lett. 453: 305-7), enzymes (Guntas and Ostermeier, 2004, J. Mol. Biol. 336: 263-73) and bioluminescent molecules (Xu et al., 1999, Proc. Natl. Acad. Sci. USA 96: 151-56) have been used as well. FRET (fluorescence resonance energy transfer) refers to a quantum mechanical effect between a given pair of chromophores, consisting of a fluorescence donor and respective acceptor. Prerequisites for FRET are proximity of donor and acceptor, and overlap between the donor emission spectrum and the acceptor excitation spectrum. When the donor and acceptor are in close enough vicinity, the emission of the excited donor decreases while emission of the sensitized acceptor increases (see Fehr et al., 2004, Current Opinion in Plant Biology 7: 345-51, herein incorporated by reference in its entirety).
There are two general types of FRET used by biosensors: intermolecular and intramolecular (Truong and Ikura, 2001, Current Opinion in Structural Biology 11: 573-78, herein incorporated by reference). Intermolecular FRET occurs when the fluorescent donor and acceptor molecules are on different macromolecules. This form of FRET is difficult to quantitate because the stoichiometry of acceptors to donors can vary with transfection efficiencies and expression levels. Nevertheless, several examples of intermolecular FRET have been reported (for a review, see Truong and Ikura, 2001; and Wouters et al., 2001, TRENDS in Cell Biol. 11(5): 203-11).
Intramolecular FRET occurs when both the donor and acceptor molecules are fused to the same molecule. In this type of sensor, the binding domains must undergo conformational changes that are large enough to translate metabolite binding into a change in FRET. Ideally, sensor families should share similar three-dimensional structures but have different substrate specificities that cover a wide spectrum of substrates. Furthermore, ultra-high-affinity binding in the nanomolar range would facilitate the engineering of mutant “nanosensors” for different physiological detection ranges by site-directed mutagenesis.
Some molecular sensors additionally employ a conformational actuator (most commonly a peptide which binds to one conformational state of the recognition element), to magnify the allosteric effect upon and resulting output of the reporter element (i.e., Miyakawa et al., 1997, Nature 388: 882-87). The applicability of the method in the absence of a conformational actuator, and its generalizability to a variety of analytes, has recently been demonstrated using bacterial periplasmic binding proteins (PBPs) (Fehr et al., 2002; Fehr et al., 2003, J. Biol. Chem. 278: 19127-33; and Lager et al., 2003, FEBS Lett. 553: 85-9).
Members of the bacterial PBP superfamily recognize hundreds of substrates with high affinity (atto- to low micro-molar) and specificity (Tam and Saier, 1993, Microbiol. Rev. 57: 320-46). PBPs have been shown by a variety of experimental techniques to undergo a significant conformational change upon ligand binding. Fusion of individual sugar-binding PBPs with a pair of GFP variants has produced sensors for maltose, ribose and glucose (Fehr et al., 2002; Fehr et al., 2003; and Lager et al., 2003). Moreover, PBPs bind substrates with affinities in the nanomolar range (Fehr et al., 2004). Thus, PBPs satisfy many of the criteria important for an ideal biosensor. The sensors have been used to measure sugar uptake and homeostasis in living animal cells, and sub-cellular analyte levels have been determined using nuclear-targeted versions (Fehr et al., 2004, J. Fluoresc. 14: 603-9).
Intramolecular biosensors are typically designed by fusing donor and acceptor fluorescent molecules to the amino and carboxy terminal portions of the sensor domain, respectively, which undergo a venus flytrap-like closure of two lobes upon substrate binding (see, e.g., Fehr et al, 2002; Fehr et al., 2003; Lager et al., 2003; and Truong and Ikura, 2001). Bacterial PBPs comprise two globular domains and are convenient scaffolds for designing FRET sensors (Fehr et al., 2003). The binding site is located in the cleft between the domains, and upon binding, the two domains engulf the substrate and undergo a hinge-twist motion (Quiocho and Ledvina, 1996, Mol. Microbiol. 20: 17-25).
PBPs can be divided into two types based on different topological arrangements of the central β-sheets and position of the termini (Fukami-Kobayashi et al., 1999, J. Mol. Biol. 286: 279-290). Maltose binding protein (MBP) is a type II binding protein, with termini being located at the distal ends of the lobes relative to the hinge region. A comparison of the crystal structures of bound and unbound states shows that the hinge-twist motion brings the termini closer together. As would be expected in the case of maltose sensor, the decrease in distance upon maltose binding leads to increased FRET between attached chromophores (Fehr et al., 2002).
In GGBP (D-GalactoseD-Glucose Binding Protein) (a type I PBP), termini are located at the proximal ends of the two lobes (Fehr et al., 2004). Thus, because of the different chromophore positions, the substrate-induced hinge-twist motion is predicted to move the attached chromophores further apart, causing a decrease in FRET. Nevertheless, type I PBPs such as GGBP have also been used to construct efficient FRET biosensors containing terminally fused donor and acceptor fluorophores (Fehr et al., 2003).
The present inventors have now surprisingly found that fusion of fluorescent domains to internal positions of a ligand binding protein, even within the same lobe of a PBP sensor, facilitates the design of an efficient biosensor that demonstrates a similar ligand affinity and a substantially larger delta ratio than its terminally fused counterpart. This is counterintuitive in view of the general model for intramolecular FRET sensors, wherein the donor and acceptor molecules are fused to separate termini on separate lobes of the protein in order to maximize the change in orientation and/or distance of the donor and acceptor chromophores upon ligand binding.
The improved signal from these sensors can be ascribed to increased rigidity and thus reduced rotational averaging. The invention thus leads to an alternative approach, also disclosed herein, to improve sensors by using more rigidly conjugated reporters. To increase the rigidity and reduce rotational averaging, we deleted portions of the fusion proteins corresponding to residues not belonging to the core structure of the three contributing partners, i.e. omitting linker sequences at the fusion sites and deleting N- or C-terminal portions of either of the three modules. Consistent with the observations made for sensors using fusion of fluorescent domains to internal positions of a ligand binding protein, enhanced terminally fused sensors also showed much increased FRET ratio changes.
SUMMARY OF THE INVENTION
The present invention therefore provides improved intramolecular biosensors and nanosensors for detecting and measuring changes in analyte concentrations, particularly transporter biosensors and biosensors constructed using bacterial periplasmic binding proteins (PBPs). In particular, the invention provides intramolecular biosensors containing at least one internally fused fluorophore moiety, as well as FRET fusion constructs encoding fluorophores with increased rigidity.
For instance, the invention provides an isolated nucleic acid encoding a ligand binding fluorescent indicator comprising a ligand binding protein moiety wherein the ligand binding protein moiety is genetically fused to a donor fluorophore moiety and an acceptor fluorophore moiety, wherein fluorescence resonance energy transfer (FRET) between the donor moiety and the acceptor moiety is altered when the donor moiety is excited and the ligand binds to the ligand binding protein moiety, and wherein at least one of either said donor fluorophore moiety or said acceptor fluorophore moiety is fused to said ligand binding protein moiety at an internal site of said ligand binding protein moiety. In one embodiment, among others, the donor and acceptor fluorophore moieties are fluorescent proteins.
The invention also provides methods of improving the sensitivity of intramolecular biosensors, including terminally and internally fused biosensors. For instance, such methods may comprise the steps of (a) providing an intramolecular FRET biosensor comprising a ligand binding protein moiety, and donor and acceptor fluorescent protein moieties fused to said ligand binding protein moiety, respectively, wherein fluorescence resonance energy transfer (FRET) between the donor moiety and the acceptor moiety is altered when the donor moiety is excited and said ligand binds to the ligand binding protein moiety; and (b) altering or modifying the fusion domain between the fluorophore and ligand binding moieties, wherein said alteration results in an intramolecular FRET biosensor with improved sensitivity as compared to said biosensor without said alteration. The alteration may be an amino acid deletion, insertion or mutation that increases the rigidity of the fluorophore linkage. The invention also encompasses nucleic acid constructs produced by such methods.
Vectors, including expression vectors, and host cells comprising the inventive nucleic acids are also provided, as well as biosensor proteins encoded by the nucleic acids. Such nucleic acids, vectors, host cells and proteins may be used in methods of detecting changes in analyte levels, and in methods of identifying compounds that modulate ligand binding.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. YbeJ FLIP-E nanosensor constructs used for expression in E. coli (A and B) and neuronal cell culture (C and D) containing terminally fused fluorophores.
FIG. 2. Spectra of FLIP-E 600n sensor (fluorescent glutamate nanosensor with a Kd for glutamate of 600 nM) at three different concentrations of glutamate: 0 mM (black), at the Kd (blue), and at saturation (red). Curves share an isosbestic point at 520 nm.
FIG. 3. A hippocampal cell treated with 1 mg/ml trypsin. Images (A-D) were taken at 10 second intervals. Note that signals on the cell surface largely disappear.
FIG. 4. Emission intensity ratio change in a hippocampal cell expressing FLIP-E 600n sensor. The images are pseudo-colored to indicate the emission intensity ratio change. Open bars above the graph (A) indicate the time point of treatment (stimulation/perfusion with glutamate). Ratio images at the time points indicated by arrows are shown in panel (B), a to i. The change in emission intensity ratio was both observed upon electrical stimulation and upon perfusion with glutamate. The ratio change was not observed when perfusing with low levels of substrate (10 nM glutamate).
FIG. 5. Emission intensity ratio change in a hippocampal cell expressing FLIP-E 10μ sensor (fluorescent glutamate nanosensor with a Kd for glutamate of 10 μM). Open bars above the graph (A) indicate the time point of treatment (stimulation/perfusion with glutamate). Ratio images at the time points indicated by arrow are shown in panel (B), a to g. Electrical stimulation did not cause a large change in the emission intensity ratio, whereas perfusion with 100 μM glutamate induces a reversible ratio change (panel (B), c and e).
FIG. 6. Internally fused pRSETB FLIP-E nanosensor constructs (A and B) showing insertion site for eCFP.
FIG. 7. Graphs comparing emission intensity of FLIP-E 600n with and without glutamate (A) and FLIP-E-internally-fused with and without glutamate (B).
FIG. 8. Internally fused pRSETB FLIP-E 600n A216-cpVenus-K217 construct (A and B) showing insertion site for cpVenus.
FIG. 9. Emission intensity of internally fused FLIP-E 600n A216-cpVenus-K217 with and without glutamate.
FIG. 10. Graphs showing the ratio changes (A) and normalized ratio changes (B) of internally fused glucose nanosensors.
FIG. 11. Graphs showing titration curves (A, C, E, G, I, K, M) and spectra (B, D, F, H, J, L, N) of glucose nanosensors.
FIG. 12. Figure showing the correlation between the starting ratio in the absence of glucose and the normalized ratio change.
FIG. 13. Diagram showing the various deletions constructed in the coding sequence of FLIPglu 600μ and the corresponding delta ratios obtained.
FIG. 14. Construction of the FLII12Pglu-600μ and FLII275Pglu-4.6m deletion sensors. The N-terminal ECFP core is boxed blue. The dispensable C-terminal sequences of ECFP are underlined in blue. The flexible linker containing a KpnI restriction enzyme recognition site is shown in black. The mglB core is boxed red, while the dispensable C-terminal residues of mglB are underlined red. The EYFP core is boxed yellow, while the dispensable N-terminal residues are underlined yellow. Construct names are labeled on the left.
FIG. 15. Correlation between Δ ratio in MOPS buffer pH 7.0 (red), number of amino acid residues deleted and affinity (Kd, μM) of the FLII12Pglu-600μ deletion constructs.
FIG. 16. Sensitivity of the FLII12Pglu-600μ deletion constructs to cell culture solution, synthetic cytosols and pH. Comparison of the Δ ratio FLII12Pglu-600μ deletion constructs in MOPS pH 7.0 (black), Hanks buffer pH 7.2 (red), Mammalian cytosol pH 7.4 (blue), plant cytosol pH 7.5 (green) and MOPS pH 5.0 (purple). FLII12Pglu-10aa, FLII12Pglu-14aa, FLII12Pglu-15aa and FLII12Pglu δ6 can be seen as the sensors least affected by different buffers and low pH.
FIG. 17. Diagram showing the constructs of three intramolecular glucose sensors: FLII12Pglu-600μ; FLII12Pglu δ4aa-593μ, and FLII275Pglu-4600μ.
FIG. 18. Diagram showing the FLIP constructs in pc DNA3.1.
FIG. 19. FRET changes observed in NIH3T3 cells transformed with the improved glucose sensors. (A) Perfusion of NIH3T3-L1 cells transiently cytosolic expressing by FLII12Pglu-600μ, (B) FLII12Pglu δ4aa-593μ and (C) FLII275Pglu-4600μ. The bars indicate the presence of 10 mM glucose in the perfusion buffer.



DETAILED DESCRIPTION OF INVENTION
The following description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed inventions, or that any publication specifically or implicitly referenced is prior art.
Other objects, advantages and features of the present invention become apparent to one skilled in the art upon reviewing the specification and the drawings provided herein. Thus, further objects and advantages of the present invention will be clear from the description that follows.
Internally Fused Intramolecular Biosensors
As described above, the present inventors have surprisingly found that fusion of fluorescent domains to internal positions of a ligand binding protein, even within the same lobe of a PBP sensor, facilitates the design of an efficient biosensor that demonstrates a similar ligand affinity and a substantially larger delta ratio than its terminally fused counterpart. This is counterintuitive in view of the general model for intramolecular FRET sensors, wherein the donor and acceptor molecules are typically fused to the termini on separate lobes of the protein in order to maximize the change in orientation and/or distance of the donor and acceptor chromophores upon ligand binding.
Without being bound to any particular theory, the present inventors believe that the data supports the prediction that rotational movements play a key role in FRET. The dipoles must be oriented in a certain position to each other for efficient resonance energy transfer. However, with terminally fused donor and acceptor moieties, one commonly assumes that the peptide bonds in the linker between the three moieties are freely rotating, thus randomizing this parameter, within a cone of steric compatibility. By inserting the fluorescent moiety into an internal position of the PBP, free or limited free rotation of the fluorophore around the peptide axis in the linker sequences is prevented, or greatly reduced. Thus, in an internal fusion, the fluorescent moiety is rigidly inserted at both ends, thereby reducing free rotation and possibly explaining the higher observed delta ratio. Alternatively, more rigidly fused chromophores enable enhanced allosteric coupling between the conformational change of the binding protein and the motion of the chromophore.
Thus, the biosensors of the present invention exhibit surprisingly enhanced activities over their terminally fused counterparts. Moreover, in some cases, internally fused donor and acceptor molecules permits the measurement of FRET increases upon ligand binding using sensors that typically operate by decreased FRET upon ligand binding, such as GGBP sensors. Thus, the direction of FRET alteration may be changed by using internally fused donor and/or acceptor moieties as compared to terminally fused counterparts.
The present invention encompasses isolated nucleic acids which encode ligand binding fluorescent indicator. An isolated nucleic acid according to the present invention encodes an indicator comprising a ligand binding protein moiety, a donor fluorophore moiety fused to the ligand binding protein moiety, and an acceptor fluorophore moiety fused to the ligand binding protein moiety, wherein fluorescence resonance energy transfer (FRET) between the donor moiety and the acceptor moiety is altered when the donor moiety is excited and said ligand binds to the ligand binding protein moiety, and wherein at least one of either or both of said donor fluorophore moiety and/or said acceptor fluorophore moiety are fused to said ligand binding protein moiety at an internal site of said ligand binding protein moiety.
Either the donor fluorophore moiety or the acceptor fluorophore moiety or both may be fused to an internal site of said ligand binding protein moiety. Preferably, the donor and acceptor moieties are not fused in tandem, although the donor and acceptor moieties may be contained on the same protein domain or lobe. A domain is a portion of a protein that performs a particular function and is typically at least about 40 to about 50 amino acids in length. There may be several protein domains contained in a single protein. A “ligand binding protein moiety” according to the present invention can be a complete, naturally occurring protein sequence, or at least the ligand binding portion or portions thereof. In preferred embodiments, among others, a ligand binding moiety of the invention is at least about 40 to about 50 amino acids in length, or at least about 50 to about 100 amino acids in length, or more than about 100 amino acids in length.
Methods of Improving Sensitivity of Fret Biosensors
As described above, the invention also provides methods of improving the sensitivity of intramolecular biosensors, including terminally and internally fused biosensors. For instance, such methods may comprise the steps of (a) providing an intramolecular FRET biosensor comprising a ligand binding protein moiety, and donor and acceptor fluorescent protein moieties fused to the two termini of said ligand binding protein moiety, respectively, wherein fluorescence resonance energy transfer (FRET) between the donor moiety and the acceptor moiety is altered when the donor moiety is excited and said ligand binds to the ligand binding protein moiety; and (b) altering or modifying the fusion domain between the fluorophore and ligand binding moieties, wherein said alteration results in an intramolecular FRET biosensor with improved sensitivity as compared to said biosensor without said alteration. The alteration may be a deletion, insertion or mutation of one or more amino acids from the linker, fluorophore or ligand binding domains that increases the rigidity of the fluorophore linkage.
The disclosed methods of improving FRET biosensor sensitivity stem from the present inventors' observations regarding internally fused FRET sensors. Having learned that the reduced rotational averaging in the intramolecular insertion of a fluorophores is a general strategy to generate sensors with high ratio changes, we hypothesized that one may obtain similar results by reducing the rotational freedom of the linkage between the analyte binding domain and the fluorophores. To test the hypothesis, we systematically removed sequences that connect the core protein structure of the binding domain and the fluorophore, i.e. by removing linker sequences and/or by deleting amino acids from the ends of the analyte binding moiety and/or the fluorophores. We found that the closer coupling achieved by such deletions also leads to higher ratio changes. This concept is exemplified herein for glucose binding constructs, but is applicable to any FRET-based biosensor.
Preferably, deletions are made by deleting at least one, or at least two, or at least three, or at least four, or at least five, or at least eight, or at least ten, or at least fifteen nucleotides in a nucleic acid construct encoding said intramolecular FRET biosensor that are located in the regions encoding the linker, or fluorophore, or ligand binding domains. Deletions in different regions may be combined in a single construct to create more than one region demonstrating increased rigidity. Amino acids may also be added or mutated to increase rigidity of the biosensor and improve sensitivity. For instance, by introducing a kink by adding a proline residue or other suitable amino acid. Improved sensitivity is measured by the ratio change in FRET fluorescence upon ligand binding, and preferably increases by at least a factor of 2 as a result of said deletion.
The invention also encompasses nucleic acid constructs produced by such methods, as well as vectors and cells containing the nucleic acids as described herein. The FRET biosensors encoded by the nucleic acid constructs are also included.
Ligand Binding Moieties
Preferred ligand binding protein moieties according to the present invention, among others, are transporter proteins and ligand binding sequences thereof, for instance transporters selected from the group consisting of channels, uniporters, coporters and antiporters. Also preferred are periplasmic binding proteins (PBP), such as any of the bacterial PBPs included in Table 1 below. As described above, bacterial PBPs comprise two globular domains or lobes and are convenient scaffolds for designing FRET sensors (Fehr et al., 2003). The binding site is located in the cleft between the domains, and upon binding, the two domains engulf the substrate and undergo a hinge-twist motion (Quiocho and Ledvina, 1996, Mol. Microbiol. 20: 17-25). In type I PBPs, such as GGBP (D-GalactoseD-Glucose Binding Protein), the termini are located at the proximal ends of the two lobes that move apart upon ligand binding (Fehr et al., 2004). In type II PBPs, such as Maltose Binding Protein (MBP), the termini are located at the distal ends of the lobes relative to the hinge region and come closer together upon ligand binding. Thus, depending on the type of PBP and/or the position of the internally fused donor or acceptor moiety, FRET may increase or decrease upon ligand binding and both instances are included in the present invention.







TABLE 1







Bacterial Periplasmic Binding Proteins











Gene name
Substrate
Species
3D
Reference





AccA
agrocinopine
Agrobacterium sp.
—/—
J. Bacteriol. (1997) 179, 7559-7572


AgpE
alpha-glucosides (sucrose, maltose,
Rhizobium meliloti
—/—
J. Bacteriol. (1999) 181, 4176-4184



trehalose)


AlgQ2
alginate
Sphingomonas sp.
—/c 
J. Biol. Chem. (2003) 278, 6552-6559


AlsB
allose
E. coli
—/c 
J. Bacteriol. (1997) 179, 7631-7637






J. Mol. Biol. (1999) 286, 1519-1531


AraF
arabinose
E. coli
—/c 
J. Mol. Biol. (1987) 197, 37-46






J. Biol. Chem. (1981) 256, 13213-13217


AraS
arabinose/fructose/xylose
Sulfolobus solfataricus
—/—
Mol. Microbiol. (2001) 39, 1494-1503


ArgT
lysine/arginine/ornithine
Salmonella typhimurium
o/c
Proc. Natl. Acad. Sci. USA (1981) 78,






6038-6042






J. Biol. Chem. (1993) 268, 11348-11355


ArtI
arginine
E. coli

Mol. Microbiol. (1995) 17, 675-686


ArtJ
arginine
E. coli

Mol. Microbiol. (1995) 17, 675-686


b1310
(putative, multiple sugar)
E. coli
—/—
NCBI accession A64880


b1487
(putative, oligopeptide binding)
E. coli
—/—
NCBI accession B64902


b1516
(sugar binding protein homolog)
E. coli
—/—
NCBI accession G64905


BtuF
vitamin B12
E. coli
—/—
J. Bacteriol. (1986) 167, 928-934


CAC1474
proline/glycine/betaine
Clostridium
—/—
NCBI accession AAK79442




acetobutylicum


cbt
dicarboxylate
E. coli
—/—
J. Supramol. Struct. (1977) 7, 463-80



(succinate, malate, fumarat)


J. Biol. Chem. (1978) 253, 7826-7831






J. Biol. Chem. (1975) 250, 1600-1602


CbtA
cellobiose
Sulfoblobus solfataricus
—/—
Mol. Microbiol. (2001) 39, 1494-1503


ChvE
sugar
Agrobacterium
—/—
J. Bacteriol. (1990) 172, 1814-1822




tumefaciens


CysP
thiosulfate
E. coli
—/—
J. Bacteriol. (1990) 172, 3358-3366


DctP
C4-dicarboxylate
Rhodobacter capsulatus
—/—
Mol. Microbiol. (1991) 5, 3055-3062


DppA
dipeptides
E. coli
o/c
Biochemistry (1995) 34, 16585-16595


FbpA
iron
Neisseria gonorrhoeae
—/c 
J. Bacteriol. (1996) 178, 2145-2149


FecB
Fe(III)-dicitrate
E. coli

J. Bacteriol. (1989) 171, 2626-2633


FepB
enterobactin-Fe
E. coli
—/—
J. Bacteriol. (1989) 171, 5443-5451






Microbiology (1995) 141, 1647-1654


FhuD
ferrichydroxamate
E. coli
—/c 
Mol. Gen. Genet. (1987) 209, 49-55






Nat. Struct. Biol. (2000) 7, 287-291






Mol. Gen. Genet. (1987) 209, 49-55


FliY
cystine
E. coli
—/—
J. Bacteriol. (1996) 178, 24-34






NCBI accession P39174


GlcS
glucose/galactose/mannose
Sulfolobus solfataricus
—/—
Mol. Microbiol. (2001) 39, 1494-1503


GlnH
glutamine
E. coli
 o/—
Mol. Gen. Genet. (1986) 205, 260-9


(protein:



J. Mol. Biol. (1996) 262, 225-242


GLNBP)



J. Mol. Biol. (1998) 278, 219-229


GntX
gluconate
E. coli
—/—
J. Basic. Microbiol. (1998) 38, 395-404


HemT
haemin
Yersinia enterocolitica
—/—
Mol. Microbiol. (1994) 13, 719-732


HisJ
histidine
E. coli
—/c 
Biochemistry (1994) 33, 4769-4779


(protein:


HBP)


HitA
iron
Haemophilus influenzae
o/c
Nat. Struct. Biol. (1997) 4, 919-924






Infect. Immun. (1994) 62, 4515-25






J. Biol. Chem. (195) 270, 25142-25149


LivJ
leucine/valine/isoleucine
E. coli
—/c 
J. Biol. Chem. (1985) 260, 8257-8261






J. Mol. Biol. (1989) 206, 171-191


LivK
leucine
E. coli
—/c 
J. Biol. Chem. (1985) 260, 8257-8261


(protein:



J. Mol. Biol. (1989) 206, 193-207


LBP)


MalE
maltodextrine/maltose
E. coli
o/c
Structure (1997) 5, 997-1015


(protein:



J. Bio. I Chem. (1984) 259, 10606-13


MBP)


MglB
glucose/galactose
E. coli
—/c 
J. Mol. Biol. (1979) 133, 181-184


(protein:



Mol. Gen. Genet. (1991) 229, 453-459


GGBP)


ModA
molybdate
E. coli
—/c 
Nat. Struct. Biol. (1997) 4, 703-707






Microbiol. Res. (1995) 150, 347-361


MppA
L-alanyl-gamma-D-glutamyl-meso-
E. coli

J. Bacteriol. (1998) 180, 1215-1223



diaminopimelate


NasF
nitrate/nitrite
Klebsiella oxytoca
—/—
J. Bacteriol. (1998) 180, 1311-1322


NikA
nickel
E. coli
—/—
Mol. Microbiol. (1993) 9, 1181-1191


opBC
choline
Bacillus subtilis
—/—
Mol. Microbiol. (1999) 32, 203-216


OppA
oligopeptide
Salmonella typhimurium
o/c
Biochemistry (1997) 36, 9747-9758






Eur. J. Biochem. (1986) 158, 561-567


PhnD
alkylphosphonate
E. coli
—/—
J. Biol. Chem. (1990) 265, 4461-4471


PhoS (Psts)
phosphate
E. coli
—/c 
J. Bacteriol. (1984) 157, 772-778






Nat. Struct. Biol. (1997) 4, 519-522


PotD
putrescine/spermidine
E. coli
—/c 
J. Biol. Chem. (1996) 271, 9519-9525


PotF
polyamines
E. coli
—/c 
J. Biol. Chem. (1998) 273, 17604-17609


ProX
betaine
E. coli

J. Biol. Chem. (1987) 262, 11841-11846


rbsB
ribose
E. coli
o/c
J. Biol. Chem. (1983) 258, 12952-6






J. Mol. Biol. (1998) 279, 651-664






J. Mol. Biol. (1992) 225, 155-175


SapA
peptides
Salmonella typhimurium
—/—
EMBO J. (1993) 12, 4053-4062


Sbp
sulfate
Salmonella typhimurium
—/c 
J. Biol. Chem. (1980) 255, 4614-4618






Nature (1985) 314, 257-260


TauA
taurin
E. coli
—/—
J. Bacteriol. (1996) 178, 5438-5446


TbpA
thiamin
E. coli
—/—
J. Biol. Chem. (1998) 273, 8946-8950


TctC
tricarboxylate
Salmonella typhimurium
—/—


ThuE
trehalose/maltose/sucrose
Sinorhizobium meliloti
—/—
J. Bacteriol. (2002) 184, 2978-2986


TreS
trehalose
Sulfolobus solfataricus
—/—
Mol. Microbiol. (2001) 39, 1494-1503


tTroA
zinc
Treponema pallidum
—/c 
Gene (1997) 197, 47-64






Nat. Struct. Biol. (1999) 6, 628-633


UgpB
sn-glycerol-3-phosphate
E. coli
—/—
Mol. Microbiol. (1988) 2, 767-775


XylF
xylose
E. coli
—/—
Receptors Channels (1995) 3, 117-128


YaeC
unknown
E. coli
—/—
J Bacteriol (1992) 174, 8016-22






NCBI accession P28635


YbeJ(GltI)
glutamate/aspartate (putative,
E. coli
—/—
NCBI accession E64800



superfamily: lysine-arginine-ornithine-



binding protein)


YdcS
(putative, spermidine)
E. coli
—/—
NCBI accession P76108


(b1440)


YehZ
unknown
E. coli
—/—
NCBI accession AE000302


YejA
(putative, homology to periplasmic
E. coli
—/—
NCBI accession AAA16375



oligopeptide-binding protein -



Helicobacter pylori)


YgiS
oligopeptides
E. coli
—/—
NCBI accession Q46863


(b3020)


YhbN
unknown
E. coli
—/—
NCBI accession P38685


YhdW
(putative, amino acids)
E. coli
—/—
NCBI accession AAC76300


YliB (b0830)
(putative, peptides)
E. coli
—/—
NCBI accession P75797


YphF
(putative sugars)
E. coli
—/—
NCBI accession P77269


Ytrf
acetoin
B. subtilis
—/—
J. Bacteriol. (2000) 182, 5454-5461


ZnuA
zinc
Synechocystis
—/—
J. Mol. Biol. (2003) 333, 1061-1069









Bacterial PBPs have the ability to bind a variety of different molecules and nutrients, including sugars, amino acids, vitamins, minerals, ions, metals and peptides, as shown in Table 1. Thus, PBP-based ligand binding sensors may be designed to permit detection and quantitation of any of these molecules according to the methods of the present invention. Naturally occurring species variants of the PBPs listed in Table 1 may also be used, in addition to artificially engineered variants comprising site-specific mutations, deletions or insertions that maintain measurable ligand binding function. Variant nucleic acid sequences suitable for use in the nucleic acid constructs of the present invention will preferably have at least 70, 75, 80, 85, 90, 95, or 99% similarity or identity to the native gene sequence for a given PBP.
Suitable variant nucleic acid sequences may also hybridize to the gene for a PBP under highly stringent hybridization conditions. High stringency conditions are known in the art; see for example Maniatis et al., Molecular Cloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols in Molecular Biology, ed. Ausubel, et al., both of which are hereby incorporated by reference. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0M sodium ion, typically about 0.01 to 1.0M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g. 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g. greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
Preferred biosensors of the present invention, among others, include glutamate sensors constructed using YbeJ binding domains, and other amino acid biosensors. Such proteins may be used as neurotransmitter biosensors for detecting and measuring changes in neurotransmitter concentrations using Fluorescence Resonance Energy Transfer (FRET) (see U.S. provisional applications 60/618,179, herein incorporated by reference in their entirety). The three major categories of substances that act as neurotransmitters are (1) amino acids (primarily glutamic acid or glutamate, GABA, aspartic acid & glycine), (2) peptides (vasopressin, somatostatin, neurotensin, etc.) and (3) monoamines (norepinephrine, dopamine & serotonin) plus acetylcholine. In particular, the invention provides glutamate binding fluorescent indicators, particularly indicators comprising a glutamate binding protein moiety from the Escherichia coli glutamate/aspartate receptor, YbeJ. Additional neurotransmitter biosensors for the neurotransmitters listed above may also be prepared using the constructs and methods provided herein.
YbeJ is also known in the art as YzzK and GltI, and its DNA sequence (SEQ ID No. 27) and protein sequence (YbeJ, protein accession no. NP—415188, SEQ ID No. 28) are known. SEQ ID Nos. 1 and 2 provide alternative nucleic acid and protein sequences for YbeJ, respectively, and include additional upstream material that may be part of the full length protein. Naturally occurring homologues from other bacterial species may also be used, for instance the PA5082 gene from Pseudomonas aeruginosa, whose gene product is 70% similar to the YbeJ protein from E. coli. Any portion of the YbeJ DNA sequence which encodes a glutamate binding region may be used in the nucleic acids of the present invention. Glutamate binding portions of YbeJ or any of its homologues may be cloned into the vectors described herein and screened for activity according to the disclosed assays.
For instance, one region that is suitable for use in the nucleic acids of the present invention is provided by SEQ ID No. 3, which encodes a truncated glutamate-aspartate binding protein sequence (SEQ ID No. 4), encoding mature protein without signal peptide. A preferred internally fused intramolecular sensor according to the present invention comprises a fluorescent protein moiety inserted between amino acids corresponding to amino acids 58 and 59, and amino acid 216 and 217 of SEQ ID No. 28. In preferred embodiments, the donor fluorescent protein moiety is eCFP, however any of the donor moieties described herein may be used. In such sensors, the acceptor fluorescent protein moiety is preferably YFP VENUS or cpVenus, inserted at the C-terminus of said glutamate binding protein moiety or internally fused to said glutamate binding protein. Further, other acceptor moieties may be used, as described herein.
Preferred artificial variants of the sensors of the present invention may exhibit increased or decreased affinity for ligands, in order to expand the range of ligand concentration that can be measured. For instance, preferred artificial variants for YbeJ sensors include, among others, glutamate binding regions comprising the mutations A207G, A207P, A207K, A207M, A207S, A207C, A207R, A207V, A207L, A207Q, A207T, A207F, A207Y, A207N, A207W, A207H, A207D, and S95W. Additional artificial variants showing decreased or increased binding affinity for glutamate may be constructed by random or site-directed mutagenesis and other known mutagenesis techniques, and cloned into the vectors described herein and screened for activity according to the disclosed assays.
The sensors of the invention may also be designed with a reporter element different from a donor/acceptor pair of FRET-compatible fluorescent proteins. For instance, the ligand-binding moiety of the sensor may be fused with an enzyme in such a manner to create an allosterically regulated enzyme whose activity is regulated by a specified ligand (Guntas and Ostermeier, 2004, J. Mol. Biol. 336(1): 263-73). In addition, such an allosterically-regulated reporter domain may be divided into two or more separate and complementing halves, e.g. complementing fragments of β-lactamase (Galarneau et al., 2002, Nature Biotechnol. 20: 619-622) or of GFP (Cabantous et al., 2005, Nature Biotechnol. 23: 102-107). Any and all reporter element fragments may be fused with the ligand-binding moiety in either an end-to-end fashion (e.g. a typical fusion protein) or inserted internally into the sequence of the ligand-binding moiety (e.g. an internally-fused fluorescent protein as described herein).
Other preferred PBPs to be used in the present invention include sugar binding proteins, such as maltose binding protein (MBP) and galactose/glucose binding protein (GGBP). Glucose sensors, such as GGBP sensors of the present invention, may be used for measuring blood glucose levels, for instance in diabetes or pregnancy. Other preferred ligand-binding moieties which provide a global conformational change in response to ligand binding include, but are not limited to, nuclear hormone receptors, lipocalins, fatty acid-binding proteins, and antibodies. Also possible are inactivated enzymes, including but not limited to, hexokinase, glucokinase, ribokinase, and any other conformationally responsive enzyme or enzyme domain.
General Materials and Methods
The isolated nucleic acids of the invention may incorporate any suitable donor and acceptor fluorescent protein moieties that are capable in combination of serving as donor and acceptor moieties in FRET. Preferred donor and acceptor moieties are selected from the group consisting of GFP (green fluorescent protein), CFP (cyan fluorescent protein), BFP (blue fluorescent protein), YFP (yellow fluorescent protein), and enhanced variants thereof, with a particularly preferred embodiment provided by the donor/acceptor pair CFP/YFP-Venus, a variant of YFP with improved pH tolerance and maturation time (Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., and Miyawaki, A. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20, 87-90). An alternative is the MiCy/mKO pair with higher pH stability and a larger spectral separation (Karasawa S, Araki T, Nagai T, Mizuno H, Miyawaki A. Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer. Biochem J. 2004 381:307-12). Also suitable as either a donor or acceptor is native DsRed from a Discosoma species, an ortholog of DsRed from another genus, or a variant of a native DsRed with optimized properties (e.g. a K83M variant or DsRed2 (available from Clontech)). Criteria to consider when selecting donor and acceptor fluorescent moieties are known in the art, for instance as disclosed in U.S. Pat. No. 6,197,928, which is herein incorporated by reference in its entirety.
As used herein, the term “variant” is intended to refer to polypeptides with at least about 70%, more preferably at least 75% identity, including at least 80%, 90%, 95% or greater identity to native fluorescent molecules. Many such variants are known in the art, or can be readily prepared by random or directed mutagenesis of native fluorescent molecules (see, for example, Fradkov et al., FEBS Lett. 479:127-130 (2000)).
When the fluorophores of the biosensor contain stretches of similar or related sequence(s), the present inventors have recently discovered that gene silencing may adversely affect expression of the biosensor in certain cells and particularly whole organisms. In such instances, it is possible to modify the fluorophore coding sequences at one or more degenerate or wobble positions of the codons of each fluorophore, such that the nucleic acid sequences of the fluorophores are modified but not the encoded amino acid sequences. Alternative, one or more conservative substitutions that do not adversely affect the function of the fluorophores may also be incorporated. See PCT application PCT/US2005/036953, “Methods of Reducing Repeat-Induced Silencing of Transgene Expression and Improved Fluorescent Biosensors], which is herein incorporated by reference in its entirety.
It is also possible to use dyes for FRET, alone or in combination with one or more of the fluorophores listed above, including but not limited to TOTO dyes (Laib and Seeger, 2004, J Fluoresc. 14(2):187-91), Cy3 and Cy5 (Churchman et al., 2005, Proc Natl Acad Sci USA. 102(5): 1419-23), Texas Red, fluorescein, and tetramethylrhodamine (TAMRA) (Unruh et al., Photochem Photobiol. 2004 Oct. 1), AlexaFluor 488, to name a few, as well as fluorescent tags (see, for example, Hoffman et al., 2005, Nat. Methods 2(3): 171-76).
It is also possible to use luminescent quantum dots (QD) or pebble-coupled approaches for FRET (Clapp et al., 2005, J. Am. Chem. Soc. 127(4): 1242-50; Medintz et al., 2004, Proc. Natl. Acad. Sci. USA 101(26): 9612-17; Buck et al., 2004, Curr. Opin. Chem. Biol. 8(5): 540-6), including Surface-Enhanced Raman Scattering, where sensors are bound to the surface of nanoparticles and detection is achieved by Raman spectroscopy (Haes and Van Duyne, 2004, Expert Rev. Mol. Diagn. 4(4): 527-37).
Bioluminescence resonance energy transfer (BRET) may also be used for both in vitro and in vivo measurements, and offers the advantages of FRET without the consequences of fluorescence excitation. BRET is a naturally occurring phenomenon. For instance, when the photoprotein aequorin is purified from the jellyfish, Aequorea, it emits blue light in the absence of GFP, but when GFP and aequorin are associated as they are in vivo, GFP accepts the energy from aequorin and emits green light. In BRET, the donor fluorophore of the FRET technique is replaced by a luciferase. In the presence of a substrate, bioluminescence from the luciferase excites the acceptor fluorophore through the same Forster resonance energy transfer mechanisms described above. Thus, by using a luciferase/GFP mutant or other fluorophore combination, BRET can be used to measure protein interactions both in vivo and in vitro (see Xu et al, 1999, Proc. Natl. Acad. Sci. USA 96: 151-56, which is herein incorporated by reference).
The invention further provides vectors containing isolated nucleic acid molecules encoding improved and internally fused biosensor polypeptides as disclosed herein. Exemplary vectors include vectors derived from a virus, such as a bacteriophage, a baculovirus or a retrovirus, and vectors derived from bacteria or a combination of bacterial sequences and sequences from other organisms, such as a cosmid or a plasmid. Such vectors include expression vectors containing expression control sequences operatively linked to the nucleic acid sequence coding for the neurotransmitter biosensor. Vectors may be adapted for function in a prokaryotic cell, such as E. coli or other bacteria, or a eukaryotic cell, including yeast and animal cells. For instance, the vectors of the invention will generally contain elements such as an origin of replication compatible with the intended host cells, one or more selectable markers compatible with the intended host cells and one or more multiple cloning sites. The choice of particular elements to include in a vector will depend on factors such as the intended host cells, the insert size, whether regulated expression of the inserted sequence is desired, i.e., for instance through the use of an inducible or regulatable promoter, the desired copy number of the vector, the desired selection system, and the like. The factors involved in ensuring compatibility between a host cell and a vector for different applications are well known in the art.
Preferred vectors for use in the present invention will permit cloning of the ligand binding domain or receptor genetically fused to nucleic acids encoding donor and acceptor fluorescent molecules, resulting in expression of a chimeric or fusion protein comprising the ligand binding domain genetically fused to donor and acceptor fluorescent molecules. Exemplary vectors include the bacterial pRSET-FLIP derivatives disclosed in Fehr et al. (2002) (Visualization of maltose uptake in living yeast cells by fluorescent nanosensors. Proc. Natl. Acad. Sci. USA 99, 9846-9851), which is herein incorporated by reference in its entirety. Methods of cloning nucleic acids into vectors in the correct frame so as to express fusion proteins are well known in the art.
The chimeric internally fused nucleic acids of the present invention are preferably constructed such that either or both the donor and acceptor fluorescent moiety coding sequences are fused to internal positions of the ligand binding protein sequence upon expression in a manner such that changes in FRET between donor and acceptor may be detected upon ligand binding. Fluorescent domains can optionally be separated from the ligand binding domain by one or more flexible linker sequences. Such linker moieties are preferably between about 1 and 50 amino acid residues in length, and more preferably between about 1 and 30 amino acid residues. Linker moieties and their applications are well known in the art and described, for example, in U.S. Pat. Nos. 5,998,204 and 5,981,200, and Newton et al., Biochemistry 35:545-553 (1996). Alternatively, shortened versions of the fluorophores or the binding proteins described herein may be used.
The invention also includes host cells transfected with a vector or an expression vector of the invention, including prokaryotic cells, such as E. coli or other bacteria, or eukaryotic cells, such as yeast cells or animal cells. In another aspect, the invention features a transgenic non-human animal having a phenotype characterized by expression of the nucleic acid sequence coding for the expression of the biosensor. The phenotype is conferred by a transgene contained in the somatic and germ cells of the animal, which may be produced by (a) introducing a transgene into a zygote of an animal, the transgene comprising a DNA construct encoding the biosensor; (b) transplanting the zygote into a pseudopregnant animal; (c) allowing the zygote to develop to term; and (d) identifying at least one transgenic offspring containing the transgene. The step of introducing of the transgene into the embryo can be by introducing an embryonic stem cell containing the transgene into the embryo, or infecting the embryo with a retrovirus containing the transgene. Transgenic animals of the invention include transgenic C. elegans and transgenic mice and other animals.
The present invention also encompasses isolated improved and internally fused biosensor molecules having the properties described herein, particularly PBP-based fluorescent indicators. Such polypeptides are preferably recombinantly expressed using the nucleic acid constructs described herein. The expressed polypeptides can optionally be produced in and/or isolated from a transcription-translation system or from a recombinant cell, by biochemical and/or immunological purification methods known in the art. The polypeptides of the invention can be introduced into a lipid bilayer, such as a cellular membrane extract, or an artificial lipid bilayer (e.g. a liposome vesicle) or nanoparticle.
The present invention includes methods of detecting changes in the levels of ligands in samples, comprising (a) providing a cell expressing a nucleic acid encoding an improved or internally fused sensor according to the present invention and a sample comprising said ligand; and (b) detecting a change in FRET between said donor fluorescent protein moiety and said acceptor fluorescent protein moiety, wherein a change in FRET between said donor moiety and said acceptor moiety indicates a change in the level of said ligand in the sample. The ligand may be any suitable ligand for which a fused FRET biosensor may be constructed, including any of the ligands described herein. Preferably the ligand is one recognized by a PBP, and more preferably a bacterial PBP, such as those included in Table 1 and homologues and natural and artificial variants thereof.
The amino acid binding sensors of the present invention are useful for detecting and measuring changes in the levels of neurotransmitters in the brain or nervous system of an animal, particularly changes in the level of extracellular glutamate, which can be a signal of a disorder or disease associated with glutamate excitotoxicity. In one embodiment, the invention comprises a method of detecting changes in the level of extracellular glutamate in a sample of neurons, comprising (a) providing a cell expressing a nucleic acid encoding a glutamate binding biosensor as described herein and a sample of neurons; and (b) detecting a change in FRET between a donor fluorescent protein moiety and an acceptor fluorescent protein moiety, each covalently attached to the glutamate binding domain, wherein a change in FRET between said donor moiety and said acceptor moiety indicates a change in the level of extracellular glutamate in the sample of neurons. Alternatively, the protein may be produced in a heterologous host, e.g. in bacteria, purified and injected into organs directly or into the intercellular spaces. The protein or derivatives thereof may also be coupled to particles including quantum dots and introduced into cells or compartments.
FRET may be measured using a variety of techniques known in the art. For instance, the step of determining FRET may comprise measuring light emitted from the acceptor fluorescent protein moiety. Alternatively, the step of determining FRET may comprise measuring light emitted from the donor fluorescent protein moiety, measuring light emitted from the acceptor fluorescent protein moiety, and calculating a ratio of the light emitted from the donor fluorescent protein moiety and the light emitted from the acceptor fluorescent protein moiety. The step of determining FRET may also comprise measuring the excited state lifetime of the donor moiety or anisotropy changes (Squire A, Verveer P J, Rocks O, Bastiaens P I. J Struct Biol. 2004 July; 147(1):62-9. Red-edge anisotropy microscopy enables dynamic imaging of homo-FRET between green fluorescent proteins in cells). Such methods are known in the art and described generally in U.S. Pat. No. 6,197,928, which is herein incorporated by reference in its entirety.
The amount of ligand in a sample can be determined by determining the degree of FRET. First the sensor must be introduced into the sample. Changes in ligand concentration can be determined by monitoring FRET changes at time intervals. The amount of ligand in the sample can be quantified for example by using a calibration curve established by titration in vivo.
The sample to be analyzed by the methods of the invention may be contained in vivo, for instance in the measurement of ligand transport on the surface of cells, or in vitro, wherein ligand efflux may be measured in cell culture. Alternatively, a fluid extract from cells or tissues may be used as a sample from which ligands are detected or measured. With amino acid sensors such as glutamate sensors, such measurements may be used to detect extracellular glutamate associated with traumatic injury to said neurons, or as a possible indicator of a neurological disorder associated with glutamate excitotoxicity, including stroke, epilepsy, Huntington disease, AIDS dementia complex, and amyotrophic lateral sclerosis, among others.
Methods for detecting ligands as disclosed herein may be used to screen and identify compounds that may be used to modulate ligand receptor binding. In one embodiment, among others, the invention comprises a method of identifying a compound that modulates binding of a ligand to a receptor, comprising (a) contacting a mixture comprising a cell expressing a biosensor nucleic acid of the present invention and said ligand with one or more test compounds; and (b) determining FRET between said donor fluorescent domain and said acceptor fluorescent domain following said contacting, wherein increased or decreased FRET following said contacting indicates that said test compound is a compound that modulates ligand binding. The term “modulate” generally means that such compounds may increase or decrease or inhibit the interaction of a ligand with the ligand binding domain.
The methods of the present invention may also be used as a tool for high throughput and high content drug screening. For instance, a solid support or multiwell dish comprising the biosensors of the present invention may be used to screen multiple potential drug candidates simultaneously. Thus, the invention comprises a high throughput method of identifying compounds that modulate binding of a ligand to a receptor, comprising (a) contacting a solid support comprising at least one biosensor of the present invention, or at least one cell expressing a biosensor nucleic acid of the present invention, with said ligand and a plurality of test compounds; and (b) determining FRET between said donor fluorescent domain and said acceptor fluorescent domain following said contacting, wherein increased or decreased FRET following said contacting indicates that a particular test compound is a compound that modulates ligand binding.
In one preferred embodiment, among others, the invention provides a method of identifying a compound that modulates glutamate excitotoxicity comprising (a) contacting a glutamate biosensor or a cell expressing a glutamate biosensor as disclosed herein and a sample of neurons with one or more test compounds, and (b) determining FRET between said donor fluorescent domain and said acceptor fluorescent domain following said contacting, wherein increased or decreased FRET following said contacting indicates that said test compound is a compound that modulates glutamate excitotoxicity. The term “modulate” in this embodiment means that such compounds may increase or decrease glutamate excitotoxicity. Compounds that increase glutamate levels are targets for therapeutic intervention and treatment of disorders associated with glutamate excitotoxicity, as described above. Compounds that decrease glutamate levels may be developed into therapeutic products for the treatment of disorders associated with glutamate excitotoxicity.
The targeting of the sensor to the outer leaflet of the plasma membrane is only one embodiment of the potential applications. It demonstrates that the nanosensor can be targeted to a specific compartment. Alternatively, other targeting sequences may be used to express the sensors in other compartments such as vesicles, ER, vacuole, etc.
Expression systems comprise not only rat neurons, but also human cell lines, animal cells and organs, fungi and plant cells. The sensors can also be used to monitor levels of glutamate in fungal and plant organisms where glutamate serves as an important nitrogen compound, but potentially also a signaling molecule. Expression in bacteria may be used to monitor glutamate levels at sites of infection or in compartments in which the bacteria reside or are introduced. Specifically, bacteria or fungi expressing the sensors may serve as biosensors or as tools to identify new pesticides using a similar scheme as outlined for drug screening above.
The biosensors of the present invention can also be expressed on the surface of animal cells to determine the function of neurons. For example, in C. elegans, many of the neurons present have not been assigned a specific function. Expression of the biosensors on the surface permits visualization of neuron activity in living worms in response to stimuli, permitting assignment of function and analysis of neuronal networks. Similarly, the introduction of multiphoton probes into the brain of living mice or rats permits imaging these processes. Finally, expression in specific neurons or glia will allow the study of phenomena such as stroke or Alzheimers Disease and the effect of such disorders on glutamate levels inside neuronal cells or on their surface. Moreover, the effect of medication on localized brain areas or neuronal networks can be studied in vivo.
Finally, it is possible to use the sensors as tools to modify ligand binding, and particularly glutamate fluxes, by introducing them as artificial ligand scavengers, for instance presented on membrane or artificial lipid complexes. Artificial glutamate scavengers may be used to manipulate brain or neuron function.
The following examples are provided to describe and illustrate the present invention. As such, they should not be construed to limit the scope of the invention. Those in the art will well appreciate that many other embodiments also fall within the scope of the invention, as it is described hereinabove and in the claims.
EXAMPLES
Example 1
Construction of Nucleic Acids and Vectors
A truncated glutamate-aspartate binding protein sequence (SEQ ID No. 4), encoding mature protein without signal peptide, was amplified by PCR using E. coli K12 genomic DNA as a template. The primers used were 5′-ggtaccggaggcgccgcaggcagcacgctggacaaaatc-3′ (SEQ ID No. 5) and 5′-accggtaccggcgccgttcagtgccttgtcattcggttc-3′ (SEQ ID No. 6). The PCR fragment was cloned into the KpnI site of digested FLIPma1-25μ (Fehr et al. 2002) in pRSET vector (Invitrogen), exchanging the maltose binding protein sequence with the YbeJ sequence. The resulting plasmid was named pRSET-FLIP-E-600n (SEQ ID NO: 9).
To improve the pH and chloride tolerance and maturation of the sensor protein, the fragment containing the enhanced YFP (EYFP, CLONTECH) sequence in pRSET-FLIP-E-600n was replaced with the coding sequence of Venus, a variant of YFP with improved pH tolerance and maturation time (Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., and Miyawaki, A. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20, 87-90). Affinity mutants carrying substitutions A207G, A207P, A207K, A207M, A207S, A207C, A207R, A207V, A207L, A207Q, A207T, A207F, A207Y, A207N, A207W, A207H, A207D, and S95W were created by site-directed mutagenesis (Kunkel, T. A., Roberts, J. D., and Zakour, R. A. (1987). Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367-382).
pRSET-FLIP-E constructs (SEQ ID NOs: 9 and 10) were transferred to E. coli BL21(DE3)Gold (Stratagene) using electroporation (Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). Molecular cloning. A laboratory manual. (Cold Spring Harbor N.Y.: Cold Spring Harbor Laboratory Press). FLIP-E proteins expressed in BL21(DE3)Gold strain were extracted and purified as previously described (Fehr et al. 2002). For expression in rat primary neuronal cell culture and PC12 cell culture, FLIP-E 600n (SEQ ID NO: 13) and −10μ cassettes (SEQ ID NO: 14) were cloned into pDisplay (Invitrogen) as follows: XmaI site and SalI site were introduced on the 5′- and 3′-ends of FLIP-E cassette, respectively, by PCR. The primers used were 5′-gagcccgggatggtgagcaagggcgaggag-3′ (SEQ ID No. 7) and 5′-gaggtcgaccttgtacagctcgtccatgccgag-3′ (SEQ ID No. 8). The PCR fragments were sequenced to confirm that there was no additional PCR error, digested with XmaI/SalI, and cloned into the XmaI/SalI sites of the pDisplay vector. Cell cultures were transfected using a modified calcium phosphate transfection protocol (Xia, Z., Dudek, H., Miranti, C. K., and Greenberg, M. E. (1996). Calcium influx via the NMDA receptor induces immediate early gene transcription by a MAP kinase/ERK-dependent mechanism. J. Neurosci. 16, 5425-5436) or Lipofectamine (Invitrogen).
Example 2
In Vitro Characterization of FLIP-E Nanosensors
A DNA fragment encoding the mature YBEJ protein was fused to ECFP and the Venus sequence at the N- and C-termini, respectively (FIG. 1). Emission spectra and substrate titration curves were obtained by using monochromator microplate reader Safire (Tecan, Austria). Excitation filter was 433±12 nm, emission filters for CFP and YFP emission were 485±12, 528±12 nm, respectively. All analyses were done in 20 mM sodium phosphate buffer, pH 7.0.
Addition of glutamate resulted in an increase in CFP emission and a decrease in YFP emission, suggesting that binding of glutamate to YBEJ results in a conformational change of the chimeric protein potentially due to a relative change in the orientation of the dipoles of the fluorophores (FIG. 2). Since CFP and YFP moieties are assumed to be attached to the same lobe, we speculate that glutamate binding causes the change in dipole-dipole angle of two fluorophores. Interestingly, the ratio and ratio change were in a similar range as compared to other sensors generated so far (Fehr et al., 2002; Fehr et al., 2003; Lager et al., 2003), suggesting that distance changes may not be the primary factor in underlying the mechanisms for FRET changes. Spectra at three different glutamate concentrations (zero, Kd, saturation) reveals an isosbestic point at 520 nm (FIG. 2). The binding constant (Kd) for glutamate was determined to be 600 nM, consistent with data obtained by other methods (de Lorimier et al., 2002). Binding constants for aspartate, glutamine, asparagine were determined to be 6 μM, 100 μM, 300 μM, respectively (see Table 1, below).
In order to expand the range of concentration that can be measured by YBEJ-based glutamate nanosensors, the YBEJ moiety was mutagenized to create nanosensors with lower affinity for glutamate. It has previously been shown that conjugating various fluorophores to sites located at the perimeter of the interdomain cleft that forms the ligand binding site (named “peristeric”) changes the ligand-binding affinity in periplasmic binding proteins (de Lorimier et al., 2002). Among the residues tested, mutation of alanine 207 to lysine, methionine, serine, cysteine, arginine, valine, leucine, glutamine, threonine, phenylalanine, tyrosine, aspargine, tryptophan, histidine, aspartate (based on the YbeJ sequence provided in SEQ ID No. 28) lowered the binding affinity significantly (Table 2). In addition, the mutation of serine 95 to tryptophan, which is suggested to interact with the nitrogen of glutamate, was found to decrease the affinity of the protein. Thus, mutations introduced into the FLIPE nanosensor can yield affinity mutants suitable to cover a wide range of physiological glutamate concentrations.












TABLE 2







Kd(M)
Kd(M)
Kd(M)
Kd(M)



YbeJ
Gluta-
Aspar-
Gluta-
Aspar-


Vector
moiety
mate
tate
mine
agine







FLIPE-600n-1
WT
6 × 10 − 7
6 × 10 − 6
1 × 10 − 4
3 × 10 − 4


FLIPE-600n-2
A207G
6 × 10 − 7
4 × 10 − 6
2 × 10 − 4
n.d.


FLIPE-600n-3
A207P
6 × 10 − 7
4 × 10 − 6
2 × 10 − 4
n.d.


FLIPE-3μ
A207K
3 × 10 − 6
2 × 10 − 5
7 × 10 − 4
n.d.


FLIPE-5μ
A207M
5 × 10 − 6
3 × 10 − 5
1 × 10 − 3
n.d.


FLIPE-5μ-2
A207S
5 × 10 − 6
3 × 10 − 5
1 × 10 − 3
n.d.


FLIPE-6μ
A207C
6 × 10 − 6
5 × 10 − 5
n.d.
n.d.


FLIPE-10μ-1
A207R
1 × 10 − 5
6 × 10 − 5
1 × 10 − 3
n.d.


FLIPE-10μ-2
A207V
1 × 10 − 5
8 × 10 − 5
6 × 10 − 3
n.d.


FLIPE-30μ
A207L
3 × 10 − 5
n.d.
n.d.
n.d.


FLIPE-40μ-1
A207Q
4 × 10 − 5
2 × 10 − 4
7 × 10 − 3
n.d.


FLIPE-40μ-1
A207T
4 × 10 − 5
1 × 10 − 4
7 × 10 − 3
n.d.


FLIPE-100μ-1
S95W
1 × 10 − 4
n.d.
n.d.
n.d.


FLIPE-100μ-2
A207F
1 × 10 − 4
6 × 10 − 4
n.d.
n.d.


FLIPE-300μ
A207Y
3 × 10 − 4
5 × 10 − 4
n.d.
n.d.


FLIPE-400μ
A207N
4 × 10 − 4
1 × 10 − 3
n.d.
n.d.


FLIPE-1m
A207W
1 × 10 − 3
n.d.
n.d.
n.d.


FLIPE-2m-1
A207H
2 × 10 − 3
2 × 10 − 3
n.d.
n.d.


FLIPE-2m-2
A207D
2 × 10 − 3
9 × 10 − 4
n.d.
n.d.









Example 3
In Vivo Characterization of FLIP-E
For the in vivo characterization of FLIP-E nanosensors, FLIPE-600n and FLIPE-10μ were cloned into the mammalian expression vector pDisplay (Invitrogen, USA). The pDisplay vector carries a leader sequence which directs the protein to the secretory pathway, and the transmembrane domain which anchors the protein to the plasma membrane, displaying the protein on the extracellular face. Rat hippocampal cells and PC12 cells were transfected with pDisplay FLIPE-600n (SEQ ID NO: 11) and −10μ (SEQ ID NO: 12) constructs. FRET was imaged 24-48 hours after transfection on a fluorescent microscope (DM IRE2, Leica) with a cooled CoolSnap HQ digital camera (Photometrics). Dual emission intensity ratios were simultaneously recorded following excitation at 436 nm and splitting CFP and Venus emission by DualView with the OI-5-EM filter set (Optical Insights) and Metafluor 6.1r1 software (Universal Imaging).
The expression of FLIP-E was observed on the plasma membrane of rat hippocampal cell culture, and to some extent also in intracellular compartments, probably in compartments involved in plasma membrane targeting of plasma membrane proteins. When treated with Tyrode's buffer containing 1 mg/mL of trypsin, the majority of fluorescence on the cell surface was eliminated, demonstrating that the FLIPE protein was indeed displayed on the extracellular face of the plasma membrane as expected from the properties of the pDisplay construct (FIG. 3). The nanosensors should thus measure extracellular glutamate levels close to the cell's surface.
To quantify the intensity of CFP and Venus emission, the fluorescence intensity in the two channels in the periphery of the cell was integrated on a pixel-by-pixel basis, and the CFP/Venus ratio was calculated. When the hippocampal cells displaying FLIPE-600n (SEQ ID NO: 13) on the surface were electrically stimulated by passing current pulse, a decrease in CFP/Venus emission ratio was observed (FIG. 4 a-c), suggesting that the glutamate is released from hippocampal cells by membrane depolarization. To confirm that the ratio change is due to changes in the extracellular concentration of glutamate, the cell was perfused with increasing concentrations of glutamate. The emission intensity ratio changed in a concentration dependent manner, (FIG. 4 d-h), indicating that the FLIPE-600n (SEQ ID NO: 13) displayed on the cell surface recognizes the extracellular glutamate. The working range of the FLIP-E 600n (SEQ ID NO: 13) sensor was between 100 nM to 1 μM, which is consistent with the in vitro working range of FLIPE-600n nanosensor (SEQ ID NO:13). The CFP/Venus ratio increased when the external medium was washed away by perfusion, suggesting that the change in FRET intensity in vivo is reversible.
In contrast to the cells expressing FLIPE/600n sensor, the CFP/Venus emission intensity change was not observed in cells expressing FLIPE-10μ (SEQ ID NO: 14) upon electro-stimulation (FIG. 5). However, a ratio change was observed when the cells were perfused with higher concentrations of glutamate, (FIG. 5 c and e), suggesting that the glutamate concentration change induced by depolarization of the cell was below the working range of FLIP-E 10μ sensor.
The novel nanosensors are thus able to measure glutamate on the surface of neuronal cells and to follow the glutamate secretion of presynaptic neurons directly.
Example 4
Internally Fused YbeJ Sensor
There is currently no crystal structure for YbeJ. We homology-modeled a potential structure on the basis of existing structures of related amino acid biding proteins (His and Gln). We then predicted positions which might be permissive, i.e., sites where an insertion would not affect the overall structure of the protein. We then introduced restriction sites by site directed mutagenesis in these positions (see Table 3 below). Then the coding region for eCFP was inserted into these sites. We then looked for bacterial colonies that showed fluorescence. Only N58V-Q59N with eCFP inserted was fluorescent (based on the YbeJ sequence provided in SEQ ID No. 28). We then attached Venus at the C-terminus (FLIP-E intermol) (see FIG. 6). The affinity was tested and we saw a much larger delta ratio change and an affinity of approximately 1 μM, which is only slightly higher than the 600n version of YbeJ carrying the fluorophores at the ends (see FIG. 7).
Attempts to insert the eCFP molecule in the Ybej protein were, except for the case of N58V-Q59N, unsuccessful. We speculated that the N-terminus and C-terminus of the eCFP molecules were too far apart, resulting in destabilizing the chimera molecule by making too wide a gap in the Ybej peptide sequence. Circular permutated GFP variants, on the other hand, had N- and C-termini that were next to each other in the original protein. Therefore, we speculated that inserting permutated fluorescent protein instead of eCFP might be less harmful for protein stability. Therefore, we inserted circular permutated Venus (Nagai T. Yamada S., Tominaga T., Ichikawa M., Miyawaki A. (2004) Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins. Proc Natl Acad Sci USA. 101:10554-9) between A216 and K217 with linker sequences GNNSAG (SEQ ID NO: 30) and GSADDG (SEQ ID NO: 31). Then eCFP was fused at the N-terminus (see FIG. 8). The affinity was tested and we saw a much larger delta ratio change and an affinity of approximately 600 nM, which is unchanged from the 600n version of YbeJ carrying the fluorophores at the ends (see FIG. 9).
Without being bound to any particular theory, we believe that the data supports the prediction that rotational movements play a role in FRET. The dipoles have to be oriented in a certain position to each other for efficient resonance energy transfer. However, with terminally fused donor and acceptor moieties, commonly one assumes that the peptide bonds in the linker between the three moieties are freely rotating, thus randomizing this parameter. By inserting the fluorescent moiety into an internal position of the PBP, we prevent free or limited free rotation of the fluorophore around the peptide axis in the linker sequences. Thus, the fluorescent moiety is now rigidly inserted at both ends, thereby reducing free wiggling and possibly explaining the higher observed delta ratio.










TABLE 3





YbeJ Positions
Original
Altered Sequence
eCFP


Mutated
Sequence
(restriction site)
Fluorescence







N58V-Q59N
aatcag
gttaac (HpaI)
+


G142-G143A
ggcggc
ggcgcc (NarI)
−


G143-D144A
ggcgat
ggcgcc (NarI)
−


D144-I145
gatatc
gatatc (native EcoRV
−




site)


A149V-N150
gccgac
gttaac (HpaI)
−


N150D-L151
gacctg
gagctc (Ecl136II)
−


M177-N178H
atgaat
atgcat (BfrBI)
−









Example 5
Internally Fused GGBP Sensors
To demonstrate that internally fused FRET biosensors could be constructed using other proteins, we constructed nanosensors comprising the Escherichia coli glucose/galactose binding protein (GGBP) as a binding domain and the Aequorea Victoria green fluorescent protein variants CFP and YFP as reporter domains. Whereas YFP was either fused to the C- or N-terminus of the binding protein, CFP was inserted into various positions of the binding protein yielding a set of internally fused sensors. Each of these sensors is characterized by different relative spatial orientations of the chromophores.
Step 1: Selection of Insertion Sites in GGBP
To scan for permissive sites inside GGBP that tolerate chromophore insertions a total of 13 different sites were selected. Those sites were preferentially located on loops or at the ends of secondary structure elements that are protruding from the core protein and which show a high B-factor in the crystal structure. Sites on both lobes of GGBP were selected. To enable CFP insertions the Nru I restriction recognition sequence was introduced by site directed mutagenesis into the respective positions in the GGBP coding sequence using Kunkel's method. Table 4 depicts the selected sites in GGBP and the mutations introduced by the Nru I recognition sequence.







TABLE 4







Insertion sites and mutations in GGBP.










mutation
secondary structure











insertion sites in N-terminal domain of GGBP










Y12S D13R
Loop



P32S D33R
loop at end of helix



S46S K47R
Helix



K58S G59R
loop at end of helix



Q83S N84R
Loop



Y102S D103R
Loop



G275S K276R
Loop



T282S N283R
Loop







insertion sites in C-terminal domain of GGBP










N130S Q131R
loop at end of helix



N136S K137R
Loop



P150S G151R
Loop



G198S P199R
Loop



N226S K227R
loop at end of helix







Numbering starts with first amino acid of the mature protein lacking the 23 amino acid signal sequence.






Step 2: Insertion of CFP and Screening for Fluorescent Colonies

The CFP coding sequence was inserted into the Nru I site in GGBP by molecular cloning. The constructs were designed to permit expression of the unfinished sensors at all stages of development. Two sets of constructs were engineered that bear the same insertion sites. One set was designed to enable the N-terminal fusion with YFP, the other to enable the C-terminal fusion with YFP.
The ligation reactions were transferred into the E. Coli expression strain BL21(DE3)gold. After transformation, the bacteria were spread on plates using selective conditions for the presence of the vector. Cells were allowed to form colonies over night at 37 degree Celsius. Subsequently, the plates were transferred to 4 degree Celsius for about 10 days to facilitate chromophore maturation. Fluorescent colonies were selected for further cloning using a UV lamp or the fluorescence module of a dissecting microscope. The screening approach permits the effective and time-saving construction of a larger number of insertions in parallel. Furthermore, it offers the opportunity to identify insertions that do not fold correctly leading to very dim fluorescence of the colonies. Table 5 reflects the relative fluorescence intensity of the colonies.







TABLE 5







Relative fluorescence of bacterial colonies.


Fluorescence of colonies after insertion of CFP









fluorescence on plate












Set for C-terminal YFP fusion



pRSETB-BamHI-mglBF16A/Y12S-CFP-D13R-kpnl 3a/1
low


pRSETB-BamHI-mglBF16A/P32S-CFP-D33R-kpnl 6a/3
low


pRSETB-BamHI-mglBF16A/S46S-CFP-K47R-kpnl 11a/5
microscope visible only


pRSETB-BamHI-mglBF16A/K58S-CFP-G59R-kpnl 1d/7
microscope visible only


pRSETB-BamHI-mglBF16A/Q83S-CFP-N84R-kpnl 6d/57
microscope visible only


pRSETB-BamHI-mglBF16A/Y102S-CFP-D103R-kpnl 17a/13
microscope visible only


pRSETB-BamHI-mglBF16A/G275S-CFP-K276R-kpnl 14c/15
microscope visible only


pRSETB-BamHI-mglBF16A/T282S-CFP-N283R-kpnl 13/73
microscope visible only


pRSETB-BamHI-mglBF16A/N130S-CFP-Q131R-kpnl 17/65
microscope visible only


pRSETB-BamHI-mglBF16A/N136S-CFP-K137R-kpnl 23/69
microscope visible only


pRSETB-BamHI-mglBF16A/P150S-CFP-G151R-kpnl 25/23
microscope visible only


pRSETB-BamHI-mglBF16A/G198S-CFP-P199R-kpnl 30/26
microscope visible only


pRSETB-BamHI-mglBF16A/N226S-CFP-K227R-kpnl 33/27
microscope visible only


Set for N-terminal YFP fusion


pRSETB-kpnl-mglBF16A/Y12S-CFP-D13R-HindIII 3/29
normal


pRSETB-kpnl-mglBF16A/P32S-CFP-D33R-HindIII 3b/32
low


pRSETB-kpnl-mglBF16A/S46S-CFP-K47R-HindIII 6/34
normal


pRSETB-kpnl-mglBF16A/K58S-CFP-G59R-HindIII 5b/35
low


pRSETB-kpnl-mglBF16AQ83S-CFP-N84R-HindIII 11/37
normal


pRSETB-kpnl-mglBF16A/Y102S-CFP-D103R-HindIII 14/41
low


pRSETB-kpnl-mglBF16A/G275S-CFP-K276R-HindIII 18/43
high


pRSETB-kpnl-mglBF16A/T282S-CFP-N283R-HindIII 22/46
normal


pRSETB-kpnl-mglBF16A/N130S-CFP-Q131R-HindIII 25/47
norm


pRSETB-kpnl-mglBF16A/N136S-CFP-K137R-HindIII 29/49
low


pRSETB-kpnl-mglBF16A/P150S-CFP-G151R-HindIII 17b/51
microscope visible only


pRSETB-kpnl-mglBF16A/G198S-CFP-P199R-HindIII 33/54
microscope visible only


pRSETB-kpnl-mglBF16A/N226S-CFP-K227R/-HindIII 37/55
low





Fluorescence intensities range from microscope visible only < low < normal < high






Step 3: Fusion to YFP and Screening for Colonies Expressing Both Chromophores

The coding sequence of YFP was inserted into the expression cassettes containing the CFP insertions of step 2 by molecular cloning. Using the two sets of CFP insertions two sets of fluorescent nanosensors were obtained that bear the same insertion of CFP but have YFP attached either to their N- or C-terminus. The ligation reactions were transferred into the expression strain BL21(DE3)gold. Following growth under selective conditions the resulting colonies were used to start 200 μl cultures in a microtiter plate to screen for clones expressing both chromophores. The cultures were grown for two days at room temperature and allowed to rest for two days at 4 degrees Celsius to facilitate chromophore maturation. Subsequently the cultures were excited at the CFP excitation wavelength (433 nm) and emission intensities were recorded from 460 nm to 560 nm covering the emission peaks of CFP and YFP. Two to three clones of each nanosensor expression cassette that showed the presence of both chromophores were selected for further analysis. Small scale cultures were started to harvest the protein by Ni-NTA affinity chromatography. To analyze the ratio changes of the new nanosensors, spectra of the purified proteins were recorded in the absence and presence of 10 mM glucose and the difference in YFP/CFP emission intensity ratios were calculated. Table 6 depicts the measured ratio changes.







TABLE 6













 











Ratio changes of completed nanosensors between 0 mM and 10 mM glucose. For each nanosensor two or three clones were analysed. For missing nanosensors no clones expressing both chromophores were identified. Grey background indicates that the two chromophores are on different lobes, white background that the chromophores are on the same lobe of GGBP. Bold nanosensors were selected for further analysis.






Step 4: Analysis of Selected Nanosensors

Nanosensors with a ratio change greater 0.2 (depicted in bold letters in table 6) were selected for further analysis. Protein was purified from larger scale cultures using Ni-NTA affinity chromatography. The resulting protein extracts were titrated with increasing concentrations of glucose in a microplate based FRET assay. The affinity of the nanosensors was determined by non-linear regression of the titration curves. Furthermore, spectra were recorded in the absence, at half-saturation and saturating glucose concentrations. As a control the original nanosensor, FLIPmglBF16A, where GGBP is sandwiched between CFP and YFP, is included. To normalize the ratio change (delta ratio), the ratio change was divided by the ratio in the absence of glucose (Table 7) (see FIGS. 8 and 9).







TABLE 7







Properties of nanosensors.










ratio













sensor
absence
saturation
Δ
Δ/absence
Kd (mM)















FLIP-mglBF16A/Y12S-CFP-D13R-YFP
4.55
7.21
2.66
0.58
0.6


(SEQ ID NOs: 15 and 16)


FLIP-YFP-mglBF16A/G275S-CFP-
1.63
2.32
0.69
0.42
4.6


K276R (SEQ ID NOs: 23 and 24)


FLIP-YFP-mglBF16A/T282S-CFP-
2.11
2.55
0.44
0.21
4


N283R (SEQ ID NOs: 25 and 26)


FLIP-YFP-mglBF16A/P32S-CFP-D33R
3.4
3.84
0.44
0.13
2.2


(SEQ ID NOs: 21 and 22)


FLIP-YFP-mglBF16A/Y12S-CFP-D13R
2.6
2.33
−0.27
−0.10
1.8


(SEQ ID NOs: 19 and 20)


FLIPmglBF16A
2.95
2.6
−0.35
−0.12
0.6


FLIP-mglBF16A/G275S-CFP-K276R-
1.93
1.6
−0.33
−0.17
13.8


YFP (SEQ ID NO: 17 and 18)





Absence depicts the ratio at the absence of glucose, saturation at saturating concentrations of glucose.


Δ shows the delta ratio between saturation and absence of glucose.


Δ/absence is the normalized delta ratio.






Summary and Discussion:

Among 22 insertions, six functional glucose sensors were identified. Four sensors showed positive ratio changes upon addition of glucose. Only two displayed negative ratio changes as the original sensor FLIPmglBF16A. Four sensors had greater relative ratio changes as compared to FLIPmglBF16A. Two sensors showed relative ratio changes similar to FLIPmglBF16A. Hence, the insertion of a chromophore into the binding protein proved to be an efficient strategy to design and improve the nanosensors. Moreover, the chromophores do not have to be located on different lobes of the binding protein to yield functional sensors.
The direction and extent of a sensor's ratio change depend on the relative spatial orientation of the chromophores before and after binding of glucose. The change in spatial orientation can be a change in distance, a change in angular orientation or both. The contribution of the change in angular orientation increases, when the chromophores are fixed and cannot freely randomize prior to the transfer of energy.
Inserting CFP into the binding protein stiffens the connection between these two components of the sensor as compared to simple C- or N-terminal fusions of CFP. This has a major impact on the sensor. The stiffer connection improves the allosteric coupling between the hinge-twist motion of the binding protein and the change in spatial orientation of the chromophores. Particularly, the change in angular orientation of the chromophores is intensified, since the wobbling of CFP is reduced. Because under this condition the direction of the ratio change cannot be predicted from the change in chromophore distance alone, it follows that sensors with ratio changes in both directions were engineered by inserting CFP.
However, due to the nature of FRET, not every relative change in chromophore orientation can translate into a change in ratio. Certain combinations of relative spatial chromophore orientations exist that are completely different but lead to a similar degree of FRET. Thus despite a large spatial reorientation of the chromophores, no significant ratio change might be observed. Moreover, insertion of CFP might abolish glucose binding by GGBP and some insertions might not even fold correctly.
The chart in FIG. 10 shows the correlation between the starting ratio in the absence of glucose and the normalized ratio change and assesses the overall success rate of the insertions. Sector 1 depicts the insertions that do not fold properly. For two insertions, both the N-terminal and C-terminal YFP fusion display a low ratio and a negligible ratio change. Sector 2 harbors 8 insertions which fold correctly but do no show a significant ratio change. This can be attributed to similar degrees of FRET before and after binding of glucose or to the fact that glucose binding is abolished. The fact that at least some functional sensors show a decreased affinity towards glucose supports the assumption that by reverting mutation F16A a number of these insertions can be turned into functional sensors. Sector 3 depicts 5 sensors based on 4 different insertions that possess higher ratio changes than the original sensor FLIPmglBF16A, which is shown as a reference point.
Thus, despite the above limitations, scanning different insertion sites for CFP in GGBP appears be an efficient method to improve the sensors. Further, the fact that the chromophores can be located on the same lobe to yield a functional sensor potentially enables us to use chromophore insertions to turn virtually each binding protein or enzyme into a sensor. It may be imagined given the above data that a further increase in signal response may be obtained by internally fusing both chromophores into the ligand-binding moiety sequence. We are creating these constructs, and expect them to show further improved properties.
Example 6
Design of FRET Biosensors with Improved Sensitivity
Having learned that the reduced rotational averaging in the internal insertion of a fluorophores is a general strategy to generate sensors with high ratio changes, we hypothesized that one may obtain similar results by reducing the rotational freedom of the linkage between the analyte binding domain and the fluorophores. We thus systematically removed sequences that connect the core protein structure of the binding domain and the fluorophore, i.e. by removing linker sequences and by deleting both amino acids from the ends of the analyte binding moiety and the fluorophores. We found that close coupling also leads to higher ratio changes. This concept is exemplified for FLIPglu.
To perform the comparison, thirteen different shortened sensor proteins were generated. Deletions of up to 8 amino acids of the linker regions between the fluorophores and the analyte binding domain did not result in a marked increase of the ratio change (see FIG. 13). Further deletions were done on the C-terminus of the ECFP (6 or 9 amino acids), on the C-terminus of the mglB analyte binding domain (5 amino acids) and on the N-terminus of the EYFP (1, 2 or 6 amino acids), which resulted in an overall increase of the change in ratio in 5 of the proteins (see FIG. 12). In all cases, the core of the fluorophore determined necessary for fluorescence (amino acid 7 to 229, Li et al., 1997, JBC 272 pp. 28545) was included.
Example 7
Testing of FRET Biosensors with Improved Sensitivity In Vitro
Materials and Methods:
Linker deletions for FLIPglu Internally Fused Sensors
Two internally fused glucose sensors were chosen on the basis of their Δ ratio and affinities, FLII12Pglu-600μ and FLIIP275Pglu-4.6m. For FLII12Pglu-600μ, the linker and less well-structured domains at the termini of mglB and Citrine (together comprising the 17 amino acid “composite linker”) was systematically deleted starting at the mglB using Kunkel mutagenesis (Kunkel et al.). 17 primers were used designed to delete increasing number of amino acid residues from FLII12Pglu-600μ creating FLII12Pglu-1aa through FLII12Pglu-17aa. In addition, deletion of 16 amino acids, FLII12PgluΔ16 was also created by adding a XhoI site at residue 305 of mglB and cloning a shortened Citrine (amino acids 7-238) using XhoI and HindIII. FLII12Pglu-16aa and FLII12PgluΔ16 thus differ in a single amino acid residue at position 305 of mglB (Ala for FLII12Pglu-16aa and Leu for FLII12Pglu δ16). Two more primers were used to delete 4 and 6 amino acid residues Gly-Gly-Thr-Gly-Gly-Ala (SEQ ID NO: 32) (GGTGGTACCGGAGGCGCC (SEQ ID NO: 33)) of the plasmid derived linker between the mglB and Citrine keeping the mglB and Citrine intact (FLII12Pglu δ4 and FLII12Pglu δ6). In case of FLIIP275Pglu-4.6m, where Citrine is at the N-terminus, a single primer was used to delete 15 amino acid residues (9 from the C-terminus dispensable portion of Citrine and 6 of the plasmid derived linker connecting the Citrine and mglB) (FIG. 14).
In Vitro Analysis of Sensors
Constructs were transferred to E. coli BL21(DE3)Gold (Stratagene, USA) using electroporation, extracted and purified as previously described (Fehr et al., 2002, Proc. Natl. Acad. Sci. USA 99: 9846-9851). Emission spectra and ligand titration curves were obtained by using a monochromator microplate reader (Safire, Tecan, Austria). The excitation filter was 433/12 nm; emission filters for ECFP and EYFP (also Citrine and Venus) emission was 485/12 and 528/12 nm, respectively. All analyses for FLIPE constructs and linearly-fused FLIPglu constructs were performed in 210 mM sodium phosphate buffer, pH 7.0; analyses of FLIIXPglu were done in 20 mM MOPS buffer, pH 7.0. In order to compare the FLII12Pglu-600μ and FLIIP275Pglu-4.6m deletions better, the Citrine emission values for each was kept constant at about 20000 and the emission gain was kept constant at 80. The sensors were also analysed in Hanks buffer (pH 7.2), synthetic mammalian cytosol (pH 7.2), synthetic plant cytosol (pH 7.2) and MOPS pH 5.0 using the same amount of protein as used for assay in MOPS pH 7.0. The Kd of each sensor was determined by fitting to a single site binding isotherm: S=(r−rapo/(rsat−rapo)=[L]/(Kd+[L]), where S is saturation; [L], ligand concentration; r, ratio; rapo ratio in the absence of ligand; and rsat, ratio at saturation with ligand. Measurements were performed with at least three independent protein extracts. ECFP emission is characterized by two peaks at 485 and 502 nm; the ratio was defined here as the uncorrected fluorescence intensity at 528 nm divided by the intensity at 485 nm.
Analysis in Different Buffers
In order to see the effect of environmental conditions on the sensors, they were analysed under various conditions, in mammalian cell culture solution (Hanks buffer: 137 mM NaCl, 5.4 mM KCl, 0.3 mM Na2HPO4, 0.4 mM KH2PO4, 4.2 mM NaHCO3, 0.6 MgSO4, 10 mM Lactate, 1 mM Pyruvate pH 7.4), synthetic mammalian cytosol (135 mM K(gluconate), 4 mM KCl, 12 mM NaHCO3, 0.8 mM MgCl2, 0.2 μM CaCl2 pH 7.4), synthetic plant cytosol (10 mM NaCl, 150 mM K(gluconate), 1 mM MgCl2, 100 mg/mL BSA, 10 mM HEPES pH 7.5 with BTP) and MOPS buffer pH 5.0. The protein amount was kept constant as for the analysis in MOPS buffer pH 7.0. The spectrum was measured with no glucose, 10 mM glucose and 100 mM glucose in triplicate and the analysis was done with 2 independent protein preps for each sensor.
Results:
FLIPglu Linker Variation
To further improve the signal to noise ratio and to develop environmentally stable sensors, a systematic deletion analysis of the linkers in the intramolecular FRET sensor FLII12Pglu-600μ (Deuschle et al., 2005, Protein Science 14:2304-2314) was carried out. The glucose nanosensor FLII12Pglu-600μ consists of the mature glucose/galactose-binding protein mglB from Escherichia coli into which CFP had been inserted at position 12 and a linearly fused EYFP via a 6-amino acid linker to the C-terminus (Deuschle 2005). The linker and less well-structured domains at the termini of mglB and EYFP variants (together comprising the “composite linker”) would be assumed to allow flexible (if not free) rotation of the fluorophores relative to the binding protein and one another. The composite linker was systematically truncated in an attempt to decrease rotational averaging and to enhance the allosteric coupling. FPs possess terminal regions not absolutely required for folding and fluorescence (an N-terminal helix and a C-terminal coil) (Li et al., 1997, J. Biol. Chem. 272: 28545-28549). Furthermore, five amino acids may be deleted from the C-terminal region of the mglB binding protein without affecting binding. These together yield 17 amino acids, the removal of which might a priori be expected to preserve binding and fluorescence (FIG. 14). Composite linker regions were deleted from FLII12Pglu-600μ in a stepwise manner.
Effect of Deletions on Ratio and Kd
Most of the FLII12Pglu-600μ deletions showed a decreased FRET compared to the full length sensor. The Δ ratio of the deletion constructs varying between 0.52 (FLII12Pglu-17aa, 78% decrease) to 2.26 (FLII12Pglu-12aa, 5% decrease). Out of the 20 deletion constructs 14 still had a Δ ratio of above 1 of which 5 constructs had Δ ratio of 1.3 or more (FLII12Pglu-6aa 1.32, FLII12Pglu-7aa 1.31, FLII12Pglu-10aa 1.3, FLII12Pglu-12aa 2.26, FLII12Pglu-16aa-1.40). FLII12Pglu δ4 and FLII12Pglu δ6 had a slightly improved Δ ratio (4% increase) as compared to FLII12Pglu-600μ. Interestingly, FLII12Pglu-16aa and FLII12Pglu δ16, showed a decrease in ratio upon ligand binding whereas the FLII12Pglu-600μ and all of the other deletions show increased ratio upon ligand binding. The affinity of each of the sensors was determined by titrating with glucose (Table 8). The affinity to glucose decreased after deletion of 2 amino acids FLII12Pglu-2aa through FLII12Pglu-13aa have binding constants ranging between 1.5-2.0 mM, deletion of more than 13 amino acids further decreased the affinity (FLII12Pglu-14aa 3.4 mM, FLII12Pglu-15aa 2.6 mM). FLII12Pglu-17aa has a dramatically decreased affinity of 6.8 mM. FLII12Pglu δ4 and FLII12Pglu δ6 however have Kd comparable to FLII12Pglu-600μ (FIG. 15, Table 8).
FLIIP275Pglu-15aa showed an increased Δ ratio of 1.14 (73% increase) as compared to FLIIP275Pglu-4.6m, which has a Δ ratio of 0.66. However the deletion affected affinity dramatically, decreasing it to a point where the sensor was no longer measurable (data not shown). So, in order to make a usable sensor, the alanine-16 in the mglB, was mutated back to wild-type phenylalanine which is involved in glucose binding (Fehr et al. 2003), thus decreasing the affinity of FLIIP275Pglu-15aa to 1.5 mM and an increased Δ ratio.
The FLII12Pglu-600μ loop-inserted sensor shows a significantly higher ratio change than the linear-fusion FLIPglu-600μ sensor; with little effect on ligand affinity. Upon deletion of up to eleven residues from the sensor (first from the C-terminal helix of the mglB domain: 5 residues, then from the synthetic linker connecting the mglB and YFP domains: 6 residues), there is a slight decrease in ligand affinity, and a decrease in ligand-dependent signal change. Molecular modeling suggests that up to this point, there is still a good degree of separation between the YFP and both the N- and C-terminal lobes of mglB (the CFP is not modeled to be highly sterically regulated by any of the other domains). The N-terminal domain of mglB is modeled to be in closer proximity to the YFP in the open versus the closed conformation (modeled by overlaying the open and closed structures of the E. coli ribose-binding protein rbsB). Thus it appears that the YFP domain is coming into closer contact with the N-terminal mglB domain, perhaps making some favorable contacts, thus driving the equilibrium slightly towards the open state, and slightly decreasing affinity. Up to the −11aa deletion, signal change and ligand-binding affinity appear to be positively correlated, with higher-affinity sensors also having a higher signal change. This is consistent with the YFP domain having some sort of interaction with the N-terminal domain of mglB in the open state, with the result that affinity is decreased by shifting the equilibrium, and the ratio change is adversely affected, perhaps through quenching. After this amount of deletion, molecular modeling suggests that the YFP is coming into very close proximity to the mglB N- and C-terminal domains, and indeed the −12aa deletion appears as if it may be conformationally restricted by this proximity, resulting in decreased rotational averaging and a higher signal change. Beyond this point, signal change and ligand-binding affinity become negatively correlated, with higher-affinity sensors yielding a lower ratio change. This is consistent with the molecular modeling, and suggests that after this point, the YFP and the mglB open-form N-terminal domain come in sufficient proximity as to give rise to energetically-unfavorable clashes, thus making the closed-form more favorable and increasing affinity.
Deletions beyond 15 amino acids were most sensitive to small deletions, consistent with an overall “tightening” of the allosteric linkage between domains. In this regime, even deletion of a single amino acid reversed the sign of the fluorescence signal change. This is somewhat surprising since similar deletions in the linearly-fused FLIPglu-600Δ13 sensor did not show these dramatic effects. This suggests that perhaps there is some degree of allosteric cross-regulation between the YFP and the loop-inserted CFP, which is modeled to be about 20 Å away, giving rise to the high sensitivity to small deletions.
Effects of deletions targeted solely to the center of the synthetic linker were assayed independently (right section of FIG. 15), and had minimal effect on affinity, as would be expected (the linker is still quite long, and inter-domain contacts are not affected), and a slight increase in signal change, consistent with a slight decrease in the rotational average caused by the likely-unstructured synthetic linker, without any quenching due to deletions of the highly-structured terminal helices of the mglB and YFP domains.
Sensitivity to Environmental Conditions
It has been noted before that buffers can affect ratio change. Moreover, in vivo the ratio change is always dampened owing to various factors such as pH, presence of ions, sugars etc. Therefore, to identify the sensors best suited for in vivo applications, various buffers mimicking cell medium (Hank's), mammalian cytosol, plant cytosol and low pH similar to that inside vesicles, vacuoles or cell wall were tested (Table 8). FLII12Pglu-600μ shows a 57% to 74% decrease in ratio change in MOPS pH 5.0 and plant cytosol. Most of the deletion constructs have a 20-70% decreased Δ ratio in various buffers. Of the 5 constructs having a Δ ratio of 1.3 or more, FLII12Pglu-6aa and FLII12Pglu-7aa are greatly affected by all the buffers tested showing a decreased Δ ratio of 20-61%. FLII12Pglu-10aa is unaffected by Hanks buffer and very slightly affected in mammalian cytosol (10% decrease), it shows a 28% decrease in Δ ratio in plant cytosol and a 66% decrease in low pH. FLII12Pglu-12aa shows a decrease of 52-59% in all buffers but still has a Δ ratio of 1.0. FLII12Pglu-16aa shows a decrease of about 30% in Hanks buffer and mammalian cytosol and is unaffected in plant cytosol and MOPS pH 5.0 but, it completely changes orientation in response to different ions. It shows increase in ratio in Hanks buffer and mammalian cytosol and decrease in ratio in plant cytosol and MOPS pH 5.0 (same as FLII12Pglu δ16). FLII12Pglu-15aa however is the least affected in all the buffers and even has an improved Δ ratio in Hanks buffer and mammalian cytosol (FIG. 16).
FLIIP275Pglu-4.6m is unaffected in Hanks buffer and mammalian cytosol but shows a decreased Δ ratio in plant cytosol (28%) and MOPS pH 5.0 (82%). FLIIP275Pglu-15aa showed a 40 and 45% decrease in Hanks buffer and mammalian cytosol respectively, and a 75 and 88% decrease in plant cytosol and low pH (Table 8).
Sensors with the Highest Ratio and Resistance to Environmental Conditions
Though most of the FLII12Pglu-600μ deletion constructs have a decreased Δ ratio than the original sensor, they showed more resistance to the environmental conditions tested. The deletion of residues most likely rearranges the sensor in a way that residues most sensitive to ions are no longer exposed thus making the sensor more resistant to environmental conditions.







TABLE 8







Ratio change and affinity of the FLII12Pglu-600μ and FLII275Pglu-4.6m in MOPS buffer


pH 7.0, Hanks buffer, mammalian cytosol, plant cytosol and MOPS buffer pH 5.0














MOPS pH 7.0
Kd
HANKS BUFFER
Mamm cytosol
Plant cytosol
MOPS pH 5.0



















Sensor Name
Ratio
Stdev
(μM)
Stdev
Ratio
stdev
Ratio
stdev
Ratio
stdev
Ratio
stdev






















FLIP glu 600μ
−0.29
0.0208
583
8.49










FLII12Pglu-600μ
2.37
0.0764
675
45.25
0.84
0.2056
0.64
0.0306
0.62
0.2723
1.02
0.0354


FLII12Pglu-1aa
1.24
0.0624
796
277.89
0.64
0.0566
0.42
0.0283
0.73
0.0354
0.87
0.0707


FLII12Pglu-2aa
1.13
0.0907
1580
108.19
0.35
0.0058
0.36
0.1021
0.31
0.0569
0.94
0.1250


FLII12Pglu-3aa
0.81
0.0306
1904
376.18
0.41
0.1079
0.39
0.1380
0.24
0.0361
0.89
0.2121


FLII12Pglu-4aa
0.97
0.0586
1562
451.84
0.48
0.1002
0.48
0.1380
0.38
0.0577
0.99
0.1061


FLII12Pglu-5aa
1.15
0.0862
1465
53.03
0.55
0.0850
0.48
0.1450
0.46
0.1222
0.79
0.1273


FLII12Pglu-6aa
1.32
0.1041
1474
118.09
0.70
0.1914
0.52
0.0557
1.07
0.0751
0.78
0.1531


FLII12Pglu-7aa
1.31
0.1212
1580
113.14
0.75
0.1217
0.58
0.1997
0.53
0.0200
0.95
0.1415


FLII12Pglu-8aa
1.14
0.0306
1924
217.79
0.57
0.0854
0.58
0.0551
0.51
0.0495
0.80
0.2108


FLII12Pglu-9aa
1.03
0.0300
1600
229.81
0.59
0.0700
0.58
0.0252
0.44
0.0141
0.83
0.0757


FLII12Pglu-10aa
1.29
0.0265
1473
41.72
1.27
0.1137
1.16
0.1159
0.94
0.0212
0.44
0.0100


FLII12Pglu-11aa
0.72
0.2397
1733
333.05
0.49
0.2030
0.39
0.1701
0.26
0.2829
0.22
0.1935


FLII12Pglu-12aa
2.26
0.0493
1953
192.33
1.05
0.0700
1.07
0.0874
0.95
0.1670
0.92
0.0707


FLII12Pglu-13aa
0.58
0.1484
2007
292.04
0.50
0.1838
0.57
0.1061
0.17
0.0071
0.29
0.0778


FLII12Pglu-14aa
1.08
0.0346
3423
74.95
0.83
0.1609
0.86
0.1758
1.02
0.0379
0.43
0.1768


FLII12Pglu-15aa
1.04
0.0321
2642
260.22
1.37
0.0778
1.36
0.1626
0.99
0.2828
0.95
0.0566


FLII12Pglu-16aa
−1.40
0.0929
1235
157.68
0.46
0.0458
0.29
0.1858
−1.37
0.0495
−1.15
0.0990


FLII12Pglu-17aa
0.52
0.0513
6800
424.26
0.50
0.1365
0.51
0.1332
−0.04
0.1931
−0.09
0.0071


FLII12Pglu δ 4
2.45
0.1767
594
64.35
1.38
0.2401
1.00
0.2060
2.53
0.1290
1.29
0.1819


FLII12Pglu δ 6
2.46
0.1890
659
156.98
2.31
0.0707
2.06
0.1697
2.12
0.0495
0.93
0.0105


FLII12Pglu δ 16
−0.79
0.0100
1766
221
0.48
0.0636
0.21
0.0424
−0.61
0.0707
−1.07
0.0586


FLII275Pglu 4.6m
0.66
0.0112
5200
520
0.73
0.04
0.68
0.0707
0.62
0.1484
0.16
0.0565









Summary and Discussion:

We have accumulated a large data set following the effect residue-by-residue of a series of deletions from the binding protein (BP)-to-fluorescent protein (FP) boundary in a high-signal change loop-inserted glucose sensor FLII12Pglu-600μ. Deletions have concomitant effects both on the signal change and glucose-binding affinity of the nanosensor family, consistent with predictions from crude molecular modeling. Of all the sensor modifications, only deletions of one or two amino acids from the center of the synthetic linker connecting the mglB C-terminus with the YFP N-terminus give rise to sensors with higher signal change or higher ligand-binding affinity (in this case, both). All other deletions decrease affinity for glucose, and the glucose-dependent signal change. Some sensors give a higher signal change than the original sensor in different buffer conditions, however, which will be useful for in vivo sensing. Perhaps most importantly, the family of linker-deleted sensors provides a robust data set for the rationalization and design of further linker variants, which may allow high-response sensors to be created out of non-functional ones.
Taken together, the data set supports a model in which local allosteric regulation, particularly of reporter element orientation, plays a significant role in the resonance energy transfer of a family of genetically-encoded nanosensor proteins. Testing of this hypothesis by rational protein design produced sensors with greatly-improved signal-to-noise, enabling a wide array of in vivo applications. Molecular modeling may provide a route to further sensor improvement, and may prove useful in the optimization of other signal transduction mechanisms, such as allosteric enzymatic switches. These findings may be relevant for the optimization of other types of FRET sensors as well as the generation of novel sensors.
Example 8
Testing of FRET Biosensors with Improved Sensitivity In Vivo
To test the improved sensors for glucose detection in living cells and to test whether the sensors can be used also in other cell types, three intramolecular sensors (FLII12Pglu-6001μ; FLII12Pglu δ4aa-593μ; FLII275Pglu-4600μ; FIG. 17) were cloned into pcDNA3.1 (−) (FIG. 18). FIG. 19 shows FRET changes observed in NIH3T3 cells transformed with the improved glucose sensors.
All publications, patents and patent applications discussed herein are incorporated herein by reference. While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.

## Claims

1. An isolated nucleic acid comprising a polynucleotide sequence which encodes: a glutamate-aspartate receptor (YbeJ) comprising the amino acid sequence of SEQ, ID NO: 28, wherein the YbeJ specifically binds a glutamate or aspartate, and at least one of a donor fluorophore protein moiety fused to the YbeJ or an acceptor fluorophore protein moiety fused to the YbeJ, wherein the coding region of the donor fluorophore protein moiety is inserted between amino acids 58 and 59 of SEQ, ID NO: 28, and the coding region of the acceptor fluorophore protein moiety is inserted at an internal site of the coding region of said YbeJ.

2. The isolated nucleic acid of claim 1, wherein said coding region of the donor fluorescent protein moiety and said coding region of the acceptor fluorescent protein moiety are fused to the same lobe of said YbeJ.

3. The isolated nucleic acid of claim 1, wherein said coding region of the acceptor fluorophore protein moiety is inserted at the C-terminus of said YbeJ.

4. The isolated nucleic acid of claim 1, wherein said donor fluorophore protein moiety is selected from the group consisting of a GFP, a CFP, a BFP, a YFP, a dsRED, CoralHue Midoriishi-Cyan (MiCy) and monomeric CoralHue Kusabira-Orange (mKO).

5. The isolated nucleic acid of claim 1, wherein said acceptor fluorophore protein moiety is selected from the group consisting of a GFP, a CFP, a BFP, a YFP, a dsRED, CoralHue Midoriishi-Cyan (MiCy) and monomeric CoralHue Kusabira-Orange (mKO).

6. The isolated nucleic acid of claim 4, wherein the donor fluorophore protein moiety is eCFP.

7. The isolated nucleic acid of claim 5, wherein the acceptor fluorophore protein moiety is YFP VENUS.

8. The isolated nucleic acid of claim 1, further comprising at least one linker moiety that links the internal site of the YbeJ to the at least one donor fluorophore protein moiety or acceptor fluorophore protein moiety.

9. An expression vector comprising the nucleic acid of claim 1 or 8.

10. A cell comprising the vector of claim 9.

11. The isolated nucleic acid of claim 1, further comprising one or more nucleic acid substitutions that modify the affinity of the YbeJ to glutamate or aspartate.

12. A ligand binding fluorescent indicator encoded by the nucleic acid of claim 1 or 8.