WO2008115420A2

WO2008115420A2 - Methods for detecting molecular interactions within cells using combination of inducible promoters and biosensors

Info

Publication number: WO2008115420A2
Application number: PCT/US2008/003401
Authority: WO
Inventors: Frank J. Delfino; Christopher J. Strock; Kenneth A. Giuliano; D. Lansing Taylor; David R. Premkumar
Original assignee: Cellumen, Inc.
Priority date: 2007-03-15
Filing date: 2008-03-14
Publication date: 2008-09-25
Also published as: WO2008115420A3

Abstract

The invention provides methods and reagents for identifying an agent, such as by screening a library of agents, that modulates the interaction of s an endogenous polypeptide and a biosensor polypeptide comprising a binding domain, a localization domain and a reporter domain all of which are operably linked to an inducible promoter.

Description

METHODS FOR DETECTING MOLECULAR

INTERACTIONS WITHIN CELLS USING COMBINATION

OF INDUCIBLE PROMOTERS AND BIOSENSORS

RELATED APPLICATION This application claims the benefit of U.S. Provisional Application No.

60/894,912, filed on March 15, 2007. The entire teachings of the above application are incorporated herein by reference.

BACKGROUND OF THE INVENTION

Interactions among molecules such as proteins and their role in regulating overall cellular functions are fundamental to biochemistry. Protein-protein interactions, as well as interactions with other molecules, such as nucleic acids, carbohydrates, and lipids have been recognized as important drug targets. Such interactions can be correlated, directly or indirectly, with a variety of intracellular events, such as signal transduction, metabolism, cell motility, apoptosis, cell cycle regulation, nuclear morphology, cellular DNA content, microtubule-cytoskeleton stability, and histone phosphorylation. Although, protein-protein interactions have long been considered relevant, they are virtually intractable targets for small molecule drug discovery.

Molecular interactions and the effects of drugs or other treatments on such interactions are currently detected by methods such as in vitro assays where the interactions between purified molecular components are directly measured, two- hybrid systems and variants thereof, in vivo assays where a protein-protein interaction is directly sensed and reported (e.g., fluorescence resonance energy transfer (FRET) between two labeled proteins; incorporation of labeled molecules and detection via antibodies), prediction-based approaches where libraries of 3-D protein structures are scanned for potential protein interaction sites based on data sets composed of known protein-protein or protein-ligand interaction structures, and protein tagging and purification or protein-protein complexes followed by mass spectroscopy analysis. These methods, however, have numerous disadvantages. For example, low sensitivity of detection, large time requirements for assays, the need to construct multiple chimeric proteins, the inability to monitor molecular binding and its effects in live cells, and the need for specialized and expensive equipment, are all limitations on current detection methods. Thus, improved reagents and methods for detecting and measuring molecular binding events and their effects on other cellular functions are needed.

Detailed knowledge of the complex topography of protein-protein interaction sites has been helpful in the design of new protein-protein interaction inhibitors. However, the art lacks methods and reagents to decipher the large number of dynamically interacting protein domains that regulate cellular biochemistry, especially within the context of the living cell where these interactions are to be targeted by new drugs. Furthermore, the successful development of small molecule effectors of protein-protein interactions will need to overcome inadequate efficacy due to low affinity and toxicity resulting from non-specific protein binding (Fry, D.C. and L.T. Vassilev, JM?/ Med, 83(12):955-63 (2005)). Improved reagents and methods for detecting and measuring molecular binding events and their effects on other cellular functions are needed.

Cellular systems biology has been defined as the investigation of the integrated and interacting networks of genes, proteins, and metabolites that are responsible for normal and abnormal cell functions (Giuliano et al, Systems Cell Biology based on High-content Screening," Methods Enzymol., 414:601-19 (2006)). Cells are also the first level of biological organization that yield "emergent properties," including life. It is now clear that the one gene, one target, one pathway approach to drug discovery and basic biomedical research is an over-simplification. New methods are needed that directly approach the systems nature of life. The cell, as the basic unit of function, can be used to understand the "systems" nature of functions using advanced reagents with whole plate readers and especially high content screening (HCS).

One key element of the integrated and interacting networks of proteins is the ability of cells to regulate protein-protein interactions that play an important role in cell functions. Thus, there is a need to determine key protein-protein interactions in the same profile where multiplexed assays are used to measure other cellular parameters.

SUMMARY OF THE INVENTION

The invention provides methods and reagents for identifying an agent that modulates the interaction between two polypeptides in a cell. In a particular embodiment, the invention provides methods and reagents for identifying an agent that modulates the interaction of an endogenous polypeptide and a biosensor polypeptide. The biosensor polypeptide comprises one or more binding domains, one or more localization domains and one or more reporter domains all of which are operably linked to a inducible promoter.

The reagents and methods provide for a more accurate assessment of binding interactions in a cell (e.g., in a live cell) through the use of an inducible promoter. The methods and reagents of the invention provide advantages that reduce or eliminate problems in the existing art. The advantages include control of concentrations of the expression of the various domains of the biosensor polypeptide, control of the timing and length of expression, and absence of traditional methods that perturb cellular conditions for expression. For example, expression of a biosensor polypeptide that is not operably linked to an inducible promoter may perturb (by physical or chemical conditions) and the cell may need to adapt to there perturbations. Sometimes the adaptation of the cells is adverse such that the characteristics of the cell has changed (e.g., the cell is no longer a wild type cell). In addition, unregulated expression of a polypeptide such as a biosensor polypeptide through the use of a constitutive promoter can alter the characteristic of a cell in which it is expressed and thus, generate or provide results (artifacts) that do not reflect the nature environment (e.g., natural binding interactions) of the cell. For example, in order to maintain the ability to grow and divide, perturbed cells need to adjust various cellular systems including those regulating metabolism, signal transduction, organelle function, motility, cell -substrate attachments, replication of DNA, and control of gene expression. If adjustments to the perturbation are not appropriate, the cell will likely die through mechanisms such as apoptosis or necrosis, or the cell may enter a transformed state where survival is possible, but cell growth and division is not under normal cellular regulation.

The interaction between the endogenous polypeptide and the biosensor polypeptide, and the disruption of said interaction by an agent of interest can be detected and quantified using a variety of methods involving luminescence or fluorescence. The biosensor polypeptide comprises all or a portion of a binding domain, a reporter domain, and a localization domain, which are all operably linked to an inducible promoter. The inducible promoter allows for temporal manipulation of the interaction between the binding domain of the biosensor polypeptide and the endogenous polypeptide. These and other advantages of the invention, as well as additional inventive features, will be apparent from the description of the invention provided herein.

The invention provides a method for identifying an agent that modulates the interaction between two polypeptides in a cell that expresses an endogenous polypeptide. One of the polypeptides is a biosensor comprising a localization domain, a reporter domain and all or a portion of a binding domain that interacts with all or a portion of the other polypeptide, the endogenous polypeptide all of which are operably linked to an inducible promoter. One or more activating molecules is also introduced into the cell. The activating molecule induces expression of the biosensor polypeptide in the cell. The cell is then maintained under conditions in which the binding domain of the biosensor polypeptide interacts with the endogenous polypeptide, which results in localization of the biosensor polypeptide, to a cellular location. An agent is then introduced into the cell and the cellular location of the biosensor polypeptide is detected. A change in the cellular location of the biosensor indicates that the agent modulates the interaction between the biosensor polypeptide and the endogenous polypeptide.

In one aspect of the invention a method is provided for identifying an agent that modulates the interaction between an endogenous polypeptide; and a biosensor polypeptide comprising a binding domain, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter. The method comprises introducing into a cell the biosensor polypeptide and an activator into a cell comprising the endogenous polypeptide, wherein the activator induces expression of the biosensor polypeptide in the cell. The cell is maintained under conditions in which the binding domain of the biosensor polypeptide interacts with the endogenous protein, which results in localization of the biosensor polypeptide, to which is bound the endogenous polypeptide, to a cellular location. An agent is introduced to the cell; and the cellular location of the biosensor polypeptide is detected, wherein a change in the cellular location of the biosensor polypeptide indicates that the agent modulates the interaction of the biosensor polypeptide and the endogenous polypeptide.

Extracellular signal-regulated kinases (ERKs) or classical MAP kinases are widely expressed protein kinase intracellular signalling molecules which are involved in functions including the regulation of meiosis, mitosis, and post mitotic functions in differentiated cells. Thus, the protein kinase (ERK) is an important cellular target and can be studied utilizing the methods and reagents of the invention. In a particular aspect, the invention pertains to a method for identifying an agent that modulates the interaction between extracellular signal-regulated kinase, ERK and a polypeptide that interacts with ERK. The biosensor and one or more activating molecules are introduced into a cell that expresses ERK polypeptide. The activating molecules induces expression of the biosensor polypeptide in the cell. The cell "is maintained under conditions in which the binding domain of the biosensor polypeptide interacts with ERK. The interaction results in localization of the biosensor polypeptide to a cellular location wherein a change in the cellular location of the biosensor polypeptide as compared to the cellular location indicates that the agent modulates the interaction of the biosensor polypeptide and ERK. The biosensor polypeptide comprises all or a portion of a binding domain that interacts with all or a portion of ERK, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter. In a particular embodiment, biosensor polypeptide is encoded by SEQ ID NO: 1. The activator is ponasterone A. In another embodiment, the activating molecules comprise accessory polypeptides, and accessory polypeptides are encoded by SEQ. ID NO: 3. In a certain embodiment, the agent is 12-O-tetradecanoylphorbol- 13 -acetate (TPA). BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing will be apparent from the following more particular description of example embodiments of the invention, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments of the present invention.

FIG. 1 is a set of four distribution maps from the same sample showing multiple cell population responses for cell cycle (DNA content), chromatin condensation, and nuclear size, and the expression level of the fluorescent protein biosensor component (Y-axis). Populations of cells were binned according to their expression level of the HDM2 PPIB component (X-axis).

FIG. 2 depicts the expression vector pCLMN-259B nucleotide sequences encoding an inducible ERK biosensor (SEQ ID NO 1) The components of the biosensor coding region are as follows: nucleotides 1-174: 5XE/GRE control region of the inducible promoter; nucleotides 181 -475 : Eukaryotic HSP minimal promoter region of the inducible promoter; nucleotides 498-1211: ERK biosensor reporter domain (TagGFP); nucleotides 1263-1427: ERK biosensor localization domain (regulates nucleus-cytoplasm shuttling; nucleotides 1485-1538: ERK biosensor binding domain (encodes polypeptide that binds activated ERK). FIG. 3 is a schematic of an annotated map of the expression vector pCLMN-

259B encoding an inducible ERK biosensor.

FIGs. 4.1 and 4.2 depict the expression vector ERV3 nucleotide sequences encoding accessory proteins that enable inducible expression of the ERK biosensor.(SEQ ID NO: 2) FIG. 5 is an annotated map of the expression vector pERV3 encoding accessory proteins that enable inducible expression of the ERK biosensor.

FIG. 6 are a series of micrographs that depicts example responses of cell expressing the inducible ERK biosensor to treatment with 1 μm 12-O- tetradecanoylphorbol-13-acetate (TPA), an upstream activator of ERK in cells. FIG. 7 shows a gene switch (as refer to as an inducible promoter) attached to a biosensor (or biosensor component) comprising the fluorescent label, JRED, which in turn is attached to NES/NLS, which in turn is attached to HDM2 (1-118), and that attached to the plasmid, pCLMN-237-D.

FIG. 8 shows a gene-switched biosensor in the OFF position wherein a RheoReceptor-1 attached to Pl is proximate P2 attached to Rheo Activator, with diverging arrows from Pl and P2 in the presence of plasmid, pNEBR-Rl, the switch component (RheoReceptor-1) proximate to the 5XRE within pNEBR-Xl does not enable the switch component RheoActivator to turn on the Gene-of-Interest.

FIG. 9 shows photographic results of (a) cells for which a Switch attached to a TagGFP, in turn attached to HDM2(FL); (b) cells for which a Switch is attached to a TagGFP, in turn attached to a p53(FL); and (c) cells for which a Switch is attached to a TagGFP, in turn attached to a p27 polypeptide.

FIG. 10 shows a Switch-ERK Biosensor method wherein an MK2NES(49 aa) component attached to NLS(7), which is in turn attached to an RSK(28aa) component, wherein the ERK associates with the RSK-NLS fragments to cause movement of the assemblage into the Cytoplasm when treated with TPA (/30 min).

FIG. 11 shows a Caspase-3 Biosensor, wherein a fluorescent protein (FP) component attached to NLS is associated and/or attached to 5xDEVD, which in turn is attached to Annexin II.

DETAILED DESCRIPTION OF THE INVENTION A description of example embodiments of the invention follows.

Numerous reagents have been developed to detect and to measure specific protein-protein interactions in living cells. Table I summarizes these approaches. In addition, other methods such as yeast two-hybrid, mammalian protein-protein interaction trap (MAPPIT) (Eyckerman, S., et al, Nat Methods,. 2(6):427-33 (2005)), and the proximity-ligation in situ assay (P-LISA) that are either not as specific or are not applied to living cells, also have shown promise (Lievens, S. and J. Taveraier, Nat Methods, 3(12):971-2(2006)).

Table I below summarizes the methods that demonstrate specific protein- protein interactions in living cells (Table I). Table I: Reagents Designed to Detect and Measure Specific Protein-Protein Interactions In Living Cells

* Protein complementation assays (PCA 's) have been developed based on other enzymes (Kerppola, T.K., Nat Methods, 2006. 3(12): 969-71). """Indication that a Gaussia luciferase might be reversible (Remy, I. and S. W. Michnick, Nat Methods, 2006. 3(12):977-9).

The important issues that must be considered in using protein-based biosensors in live cell studies have been discussed for many years (Giuliano, K.A., et al.,. Annual Review of Biophysics and Biomolecular Structure. 24:405-434(1995); Simon, J.R., and D.L. Taylor, Methods in Enzymology: 487-507 (1986). Taylor, D.L., et al, Trends in Biochemical Sciences. 9:88-91(1984) and Wang, Y.-L., et al, Methods in Cell Biology. 24: 1-1 1(1982)). However, these principles were developed at the time when covalent labeling of proteins was used and the labeled proteins were then loaded into living cells. The emergence of genetically tagging proteins with fluorescent proteins, as well as related methods, made the technology amenable to broad and simple applications. Still, some of the principles have been "lost" over time. Nevertheless, the use of fluorescent protein biosensors can yield either great insights on functions or create complex data sets heavily weighted with artifacts. The only way to assure the first of these options is to follow some important principles that evolved over the years of using fluorescence-based reagents in living cells. In fact, the principles apply to any biosensor reporter method. The proper application of protein-based biosensors can yield the sensitivity, specificity and multiplexing capability not possible with "label-free" approaches. With fluorescence imaging of living cell, while it is possible to detect single copies of fluorescent molecules, a suitable range is between about 100 copies to about I X lO⁶ copies of fluorescent molecules in singe cells. Because biosensors are based on interacting proteins, the specificity of the biosensors matches the discrimination of their protein components. Appropriate controls can be utilized to monitor any non-specific binding.

Table II lists some of the optimal characteristics of protein-based biosensors, including protein-protein interaction biosensors. Table II below lists optimal characteristics of protein-based biosensors.

Table II: Optimal Characteristics of Protein-Based Biosensors Using Fluorescence or Luminescence for Detection

Reviewing the reagents used to detect and to measure protein-protein interactions in Table I and the optimal characteristics of protein-based biosensors in • Table II suggests that the presently applied pairs of fluorescent proteins used for FRET, in general, do not yield ^"a high enough signal to noise ratio for large-scale screening. However, a recent report suggests that an improved pair of fluorescent proteins might improve this characteristic, but probably not enough for screening (You, X., et al, Proc Natl Acad Sci USA, 103(49): 18458-63(2006)). Although the optimal traits of FRET include temporal response time of the signal and reversibility, the typical levels of biosensor overexpression used to optimize the signal to noise ratio causes concern about over-whelming the native protein functions. In some cases the biosensors become "modulators" of activity, not reporters. In addition, some of the protein functions might be significantly altered by the labeling. The primary method to determine level of protein function after labeling has usually been "native" localization compared to antibody labeling. However, more functional measurements are useful. In addition, some of the protein functions might be significantly altered by the labeling. The fluorescence-based complementation reagents have the same issues as the FRET reagents, but warrant added concern over the lag time required to develop fluorescence during the refolding of the pair of complementation halves. Moreover, the refolding of the complementation partners appears to be irreversible. This latter characteristic makes the measurement of any downstream cellular responses questionable. The complementation approach must be improved by making the complementation reversible when the tagged proteins dissociate (Remy, I. and S. W. Michnick, Nat Methods, 3(12):977-9 (2006)).

The luminescence version of the complementation reagents have the same issues as the fluorescence-based complementation reagents, but with the added requirement of exogenous coelenterazine to fuel the luminescence signal. A recent report indicates that the complementation of a luciferase from Gaussia is reversible and should replace existing non-reversible luciferase methods in functional studies (Remy, I. and S.W. Michnick, Nat Methods, 3(12):977-9 (2006)). In a cellular systems biology profile, there is some question as to the effect of coelenterazine on cell function. Detailed controls on the effect of coelenterazine on a range of cell functions such as cell cycle, metabolism, etc. should be performed.

The use of Positional Biosensors/protein-protein interaction biosensors (PPIBs) appear to have fewer potential problems than the other live cell approaches to protein-protein interactions. There is still the potential of functional problems induced by over expression (see Table II). Furthermore, constitutive over expression of one or more of the biosensor components may, over time, impose selective pressure on the heterogeneous population of cells expressing various levels of the biosensor. That is, populations of cells have the potential to adapt to perturbing expression levels of protein-based biosensor components. Cells can permanently alter the regulation of one or more cellular systems (e.g., signal transduction, metabolism, other protein-protein interactions, etc.) to accommodate the toxic activity or activities induced by over expressed biosensor components. As shown herein, advantages include control over limiting the expression level of biosensor components as well as the length of time that biosensor components are expressed within the host cells. This temporal control provides optimal cellular models for cellular systems biology profiling reagents and methods. Manipulating expression reduces or minimizes toxicity and provides sensitivity, specificity and multiplexing capabilities.

The invention provides a method for identifying an agent that modulates the interaction between two polypeptides in a cell that expresses an endogenous polypeptide. One of the polypeptides is a biosensor comprising a localization domain, a reporter domain and all or a portion of a binding domain that interacts with all or a portion of the other polypeptide, the endogenous polypeptide all of which are operably linked to an inducible promoter. One or more activating molecules is also introduced into the cell. The activating molecule induces expression of the biosensor polypeptide in the cell. The cell is then maintained under conditions in which the binding domain of the biosensor polypeptide interacts with the endogenous polypeptide, which results in localization of the biosensor polypeptide, to a cellular location. An agent is then introduced into the cell and the cellular location of the biosensor polypeptide is detected. A change in the cellular location of the biosensor indicates that^" the agent modulates the interaction between the biosensor polypeptide and the endogenous polypeptide.

The invention provides methods and reagents for identifying an agent that modulates the interaction of an endogenous polypeptide and a biosensor polypeptide. The endogenous polypeptide for use in the methods of the invention may be a naturally occurring polypeptide or protein normally expressed in the cell. In addition, variants, or fragments of such naturally occurring polypeptides can be used in the methods. The endogenous polypeptide for use in the invention may be an endogenous polypeptide that is a member of a metabolic pathway or other target for drug discovery and development.

For example, protein kinases, in particular, ERKs are endogenous polypeptides useful in the methods of the invention. Metabolic enzymes that interact with other proteins such as those involved in carbohydrate anabolism or catabolism are also useful in the methods of the invention, for example, phosphofructokinase, succinate dehydrogenase, and enolase. proteases such as caspase are another class of proteins useful in the methods of the invention. Other kinases such as p38, JNK, PKS, PDKl , cylinA-cdk2, cyclinE-cdk2, c-Abl, Src, JAKl, JAK2, JAK3, SHP-2, and CBP endogenous molecules for which inducible biosensors can be designed. Transcription factors such as NF-κB, ATF-2, and c-fos are potential targets for biosensor design. Tumor suppressors such as p53, Rb, and PTEN can also be used as targets for biosensors. In other embodiments, the endogenous polypeptide can be a disease- associated molecule such as a polypeptide related or associated with a disease, for example, a neurodegenerative disease-associated molecule, a cancer-associated molecule, infectious disease, gastrointestinal disease, cardiac disease, vascular disease, respiratory disease, pathologic inflammation, endocrine disease or a immunologic disease. Such molecules are known in the art. The polypeptide can be a polypeptide normally found in a cell, but is in abnormal quantities, conformation or location in a diseased cell, a truncated polypeptide or cleavage product of a normal polypeptide or protein, an abnormally hyper- or hypo-phosphorylated protein ( e.g., tau, kinase receptors (for example, tyrosine kinase receptor: insulin receptor, and DNA interacting proteins such as histones and the like). The disease can be (e.g., Alzheimer's disease, amyotrophic lateral sclerosis, ataxia telangiectasia, Creutzfeldt- Jakob disease, Huntington disease, multiple sclerosis, Parkinson disease, primary lateral sclerosis and the like. Neurodegenerative disease associated proteins are known in the art, and include tau, p25/cdk5, etc. The biosensor polypeptide for use in the methods of the invention is comprised of a binding domain, a localization domain and a reporter domain, all of which are operably linked to an inducible promoter. The biosensor polypeptides can be prepared by methods known to those of ordinary skill in the art. Embodiments of the invention can include providing genetic vectors (e.g., plasmids) comprising sequences encoding the biosensor polypeptide, which can be introduced into a cell in accordance with the inventive method.

According to one aspect of the invention, the biosensor polypeptide comprises, consists, or consists essentially of an interaction or binding domain, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter. Different biosensors and biosensor components that may be adapted for use in the methods of the invention have been described previously, see, e.g., WO2006/017751, the teachings of which are incorporated herein by reference in their entirety.

As used herein, a "binding domain" is a region of all or a portion of a polypeptide that is sufficient to interact with (e.g, bind to ) all or a portion of a domain of an endogenous polypeptide. As one of skill in the art will understand, the binding domain "interacts with" the endogenous polypeptide by e.g., covalent, non covalent binding.

The binding domain is a region of a biosensor polypeptide to which a domain of an endogenous polypeptide interacts. The binding domain can comprise more than just a binding domain, e.g., polypeptide sequences that do not comprise a binding domain, or amino acid sequences that flank a binding domain. Alternatively, the binding domain can consist essentially of the polypeptide sequence necessary for binding to the endogenous polypeptide. In another embodiment, less than the entire binding domain (e.g., a portion) that retains the ability to bind to the endogenous polypeptide can also be used. Binding may be by covalent or non-covalent interaction. Such binding domains can be a binding domain isolated from known polypeptides, a putative binding domain or recombinantly prepared or artificially synthesized binding domain. For example, the binding domain can be a binding domain of a polypeptide present in a normal (wUd type) cell, molecule, a disease-associated polypeptide, a non-disease-associated polypeptide, a cell cycle associated polypeptide, a tissue-specific polypeptide, and the like.

In one aspect, the binding domain comprises all or a portion of the binding domain of the protein kinase, ERK. One ERK binding domain is encoded by a portion of SEQ ID NO: 1, nucleotides 1485 to 1538.

Such binding domains may include full-length proteins, or fragments thereof. Such fragments comprise at least a portion of a binding domain of the protein. In one embodiment, the binding domain can comprise a molecule (e.g., a protein or a polypeptide) that has been mutated to change or alter one or more activities of the protein or polypeptide. For example, a binding domain can comprise all or part of a binding domain of a kinase wherein the kinase is a kinase-inactive or kinase-dead mutant. Such mutants can be useful where the activity of the molecule may otherwise be toxic to a cell.

In one aspect, the binding domain comprises all or a portion of one or the other of any interacting protein pair or complex containing a larger number of interacting protein. One example includes ATM kinase interacting with histone H2AX, the kinase Chk2, E2FI, the tumor suppressors p53 or Brcal, and other proteins such as NBSl, FancDs, Smcl, Rad9, Radl7, Strap, Mdcl, 53BpI, Artemis, or Chel . Another example is the heast shock protein Hsp90 interacting with p53, Cdc37, aurora B, JNK, MEK, PDKl, alpha-synuclein, tau protein, mdm2, or calmodulin.

In another aspect, the binding domain comprise all or a portion of the binding domain of p35, p25, cyclin dependent kinase 5 (cdk5), p53, human double minute 2 (HDM2), and the like. In one embodiment, a binding domain comprises all or part of a CDK5 dominant-negative (CDK5DN) mutant. In a particular embodiment, the CDK5DN is a CDK5DN(T33, N144) mutant.

As described herein, a biosensor polypeptide of the invention also comprises a localization domain. As used herein, a "localization domain" includes a region of polypeptide sequence that provides a selection for cellular distribution (directs the cellular localization of the polypeptide to which it is attached) of the polypeptide to one or more particular cellular locations or subcellular compartments of the cell. As used herein, a "cellular location" refers to any structural or sub-structural macromolecular component of the cell, whether it is made of protein, lipid, carbohydrate, or nucleic acid. For example, a cellular location can be a macromolecular assembly or an organelle (a membrane delineated cellular compartment). Cellular locations include, but are not limited to locations such as cytoplasm, nucleus, nucleolus, the nuclear envelope, regions within the nucleus with localized activities such as transcription, cytoskeleton, inner membrane (e.g., plasma, nuclear), outer plasma membrane, (e.g., plasma) mitochondrial membrane, inner mitochondria, Golgi, endoplasmic reticulum, lysosomes, endocytic vesicles, and extracellular space. In one embodiment, the localization domain is selected from the group consisting of a nuclear localization domain, a nucleolar localization domain, a cytoplasmic localization domain, an organellar localization domain (such as a mitochondrial, peroxisomal and/or centrosomal), and a combination thereof.

For example, the localization domain of the biosensor polypeptide is a nuclear localization domain and its target location is the nucleus. Accordingly, localization domain of the biosensor polypeptide directs the location of the polypeptide to a particular area of the nucleus when bound to the endogenous polypeptide (e.g., nucleolus, the nuclear membrane). When an agent modulates the interaction between the biosensor polypeptide of the invention and the endogenous polypeptide, the location of the biosensor polypeptide (if no longer bound to the endogenous protein) translocates (changes) from the nucleus to the cytoplasm.

Such localization domains are known to those of skill in the art and can be isolated, recombinantly prepared or artificially synthesized using standard techniques. For example, a nuclear localization sequence (NLS) domain can comprise all or a portion of the HIV protein rev, all or a portion of the nuclear localization sequence of SV40, the nuclear localization domain RRKRQK (SEQ ID NO: 3) of NFkB p50 (Henkel et al, Cell 68,1121-1 133(1992)), the nucleolar localization domain KRIRTYLKSCRRMKRSGFEMSRPIPSHLT (SEQ ID NO: 4) (Ueki, et al, Biochem Biophys Res Commun. 252:97-102, (1998), and the like. Other localization domains are known in the art, see e.g., U.S. Patent No. 7,244,614, the teachings of which are incorporated herein by reference in their entirety.

Nuclear export sequences (NES) can comprise the nuclear export sequence of mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP2), Annexin II, IkB-alpha (e.g., CIQQQLGQLTLENL (SEQ ID NO: 5), Jans et al, BioEssays, 22:532-544 (2000)), PKI-alpha (e.g., ELALKLAGLDI (SEQ ID NO: 6), Jans et al, BioEssays, 22:532-544(2000)), HIV Rev (e.g., LQLPPLERLTL (SEQ ID NO: 7), Jans et al , BioEssays, 22:532-544(2000)), MAPKK (e.g., ALQKKLEELELD (SEQ ID NO: 8), Jans et al , BioEssays (2000) 22:532-544). hNet (e.g., TLWQFLLHLLLD (SEQ ID NO 9:), Ducret et al, MoI. Cell Biol. (1999) 19:7076-7087), and the like. Combination NES/NLS localization domains are also known in the art and shuttle the polypeptide to which the localization domain is attached between the cytoplasm and nucleus. As described herein, a biosensor polypeptide of the invention also comprises a reporter domain. As known to those of skill in the art, a reporter domain provides a means to detect, assess, evaluate the polypeptide in a cell, e.g., the location of a polypeptide in a cell. The reporter domain can comprise any suitable reporter domain known to those of skill in the art. For example, a suitable reporter domain can be a fluorescent protein (e.g., BFP, GFP, RFP) or a tag (e.g., SNAP tag, Halo tag, Lumio tag, a FlAsH tag, an epitope tags (e.g., HA, myc, flag, etc.), or a combination thereof. A reporter domain can be evaluated (e.g., detected, quantified, localized such as within a cell) using standard techniques, such as detection of fluorescence or luminescence, including detection of fluorescence resonance energy transfer (FRET), fluorescence anisotropy, fluorescence rotational difference, fluorescence lifetime change, fluorescence solvent sensitivity, fluorescence quenching, bioluminescence, chemiluminescence, and the like.

As described herein, a biosensor polypeptide of the invention also comprises a operably linked "inducible promoter." In one embodiment, an inducible promoter is also referred to as a "gene switch. " An "inducible promoter" as used herein is intended to mean a promoter that is induced or controlled by interaction one or more activating molecules. As used herein, activating molecules include activators and accessory molecules or accessory polypeptides An "activator", as used herein, can be a molecule (e.g., a chemical) that interacts with the promoter and causes the promoter to express the operably linked biosensor polypeptide. Examples of activators include antibiotics (e.g., tetracycline), steroids (e.g., pontasterone A) , hormones, toxins, and the like. Other activators are synthetic small molecules, sometimes referred to as ligands, such as diacylhydrazine, psf-(2-ethyl-3-methoxybenzoyl)-N'-(3,5-dimethylbenzoyl)-N'-tert- butylhydrazine, known as RSLl .

In addition, the inducible promoter can be activated by a particular condition (physical condition). Thus, as used herein the 'activator can be a stressor (e.g., increased/decreased termperature). as will also be appreciated by those of skill in the art, tissue or cell suppressor promoter that limit the expression of an operably linked gene to certain tissues or cells. An advantage of using an inducible promoter is that the promoter can be switched on or off promoter. In the presence of activating molecules, , the promoter is "on" until the molecules are no longer present. Alternatively, in the absence of a activating molecule the promoter is "off and remains transcriptionally inactive or "off until activated with the activator. Thus, the activator can be used to regulate the amount and timing of the biosensor polypeptide expression. The control of the concentration and amount of activator accordingly controls the amount of expression of the biosensor polypeptide.

The inducible promoter comprises regulatory elements for function and expression of an operably linked biosensor polypeptide. "Operably linked" as used herein, refers to the functional relationship between the inducible promoter and the biosensor polypeptide. For example, the inducible promoter is operably linked to the other portions of the biosensor polypeptide such that it controls the expression of the other portions (domains) of the biosensor polypeptide Also included with the inducible promoter are additional components accessory proteins for expression of the biosensor polypeptide. "Accessory proteins" as used herein, include proteins that are included with the "inducible promoter for expression. Examples of accessory proteins include the advanced transctivator protein (rtTA-advanced) which is a fusion of a modified version of the bacterial Tet repressor and three repeats of the viral, VP 16 transactivation domain. Other accessory proteins include the lacl and TetR repressor proteins, the CymR protein and the proteins ZF3 and R_HS.

In certain aspects of the invention, the inducible promoter is a chemical based promoter, wherein the activator is tetracycline and the presence of the activator with the cell causes controlled expression of the biosensor polypeptide. In certain aspects of the invention, the inducible promoter is an ecdysone based inducible promoter where an activator, such as the insect steroid hormone, ponasterone A, causes controlled expression of the biosensor polypeptide.

An example of an ecdysone-based inducible promoter is the Rheoswitch® mammalian inducible expression system (NewEngland Biolabs) described in FIG. 8. It is composed of an engineered nuclear receptor and an highly specific activator. The activator, diacylhydrazine, [N-(2-ethyl-3-methoxybenzoyl)-N'-(3,5- dimethylbenzoyl)-N'-tert-butylhydrazine], know as RSLl ligand is a synthetic ligand that has no pleiotropic effects on host cells. The synthetic receptor is composed of two proteins, RheoReceptor-1 and RheoActivator, that dimerize to make a holoreceptor. Both are expressed from strong constitutive promoters on plasmid pNEBR-Rl . The RheoReceptor-1 protein is a highly engineered ligand- binding domain (LBD) of an insect EcR nuclear receptor fused to the yeast GAL4 DNA binding domain (GAL 4 is a nuclear protein that is a positive regulator of gene expression for the galactose-induced genes). The RheoActivator protein is an insect/mammalian RXR (retinoid X receptor) hybrid LBD fused to the viral activation domain VP 16. The gene to be expressed is cloned into the pNEBR-Xl plasmid under control of five tandem repeats of the GAL4 response element (5XRE). In the absence of RSLl ligand, the receptor represses transcription by binding to the GAL4 elements in a transcriptionally inactive conformation. Upon induction, the RSLl ligand tightly binds and changes the conformation of the RheoReceptor-1 protein which stabilizes the holoreceptor heterodimer on the 5XRE. The activated holoreceptor and the VP 16 activation domain bind and recruit to the promoter transcriptional coactivators along with basal machinery, resulting in a highly induced transcriptional state of the protein of interest. (Karzenowski, D., Potter, D.W., and Padidam, M. BioTechniques 39, 191-196(2005); Dai_., X., et al.,. Protein Expr. Purif. 42, 236-245 (2005); and Palli, S.R., et al, Eur. J. Biochem. 270, 1308-131(2003)).

Another example is the Ecdysone Inducible Expression System This expression system is similar to the RheoSwitch inducible promoter described above (originally available from Invitrogen) The Ecdysone Inducible Expression System is composed of the plasmids pVgRXR and pIND and the activator, Ponasterone A. The pVgRXR vector expresses a heterodimeric receptor composed of wild-type retinoid-X-receptor (RXR) and VgEcR subunits. VgEcR is a fusion protein that includes the D. melanogaster ecdysone receptor ligand binding and dimerization domains, a modified glucocorticoid receptor DNA-binding domain, and the herpes simplex virus VP 16 activation domain. The pIND vector expresses the gene of interest under the control of a minimal heat shock protein promoter, and 5 modified copies of the ecdysone response element (EcRE). In the off state, the inactive heterodimer binds to EcRE sites and tightly represses transcription via corepressor recruitment. Upon receptor binding to the ligand Ponasterone A, the corepressers are released and coactivators are recruited resulting in expression of the gene of interest. (No, D., Yao, T. P. and Evans, R. M. Proc NatlAcadSci USA 93(8):3346-51(1996);

Wyborski, D. L. and Vaillancourt, P. Strategies 12(1):1-4(1999); and Chen, J. D., Umesono, K. and Evans, R. M. Proc Natl Acad Sci USA, 93(15): 7567-71(1996)).

Yet another example of an inducible promoter is the Complete Control Inducible Mammalian Expression System (Stratagene). This system is similar to the promoter above but also includes three SpI binding sites

Another example of an inducible promoter is the Tet-On Advanced Inducible Gene Expression System (Clontech). The Tet-On Advanced Inducible Gene Expression System is composed of the plasmids pTet-On- Advanced and pTRE-Tight and the ligand doxycycline. The pTet-On-Advanced plasmid expresses the Tet-On Advanced transactivator protein (rtTA- Advanced) which is a fusion of a modified version of the bacterial Tet Repressor (TetR) and three repeats of the VP 16 transactivation domain. The pTRE-Tight vector expresses the gene of interest under the control of a modified minimal CMV promoter and a modified tetracycline response element (TRE). In the absence of doxycycline, rtTA-advanced fails to associate with the TRE and transcription is tightly repressed. Upon rtTA-advanced interaction with the ligand doxycylcine, this complex binds tightly to the TRE and efficiently activates transcription of the gene of interest. (Gossen, M. & Bujard, H. Efficacy oftetracycline-controlledgene expression is influenced by cell type, BioTechniques 89:213-215(1995); Urlinger, S., Baron, U., Thellmann, M., Hasan, M. T., Bujard, H. & Hillen, W. (2000) Exploring the sequence space for tetracycline- dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. USA 97(14):7963-7968; and Hillen, W. & Berens, C. (1994) Mechanisms underlying expression of TnlO-encoded tetracycline resistance. Annual. Rev. Microbiol. 48:345-369. Another example of an inducible promoter is the Tet-Off Advanced

Inducible Gene Expression System (Clontech) This system is similar to Tet-On except the Tet repressor portion of the rTA- advanced fusion protein is not modified and therefore binds to the TRE in the presence of doxycycline. When the rTA-doxycycline associates with the TRE, transcription is tightly repressed (off state). Upon removal of doxycycline, rTA no longer associates with the TRE and transcriptional repression is released allowing expression of the gene of interest. (Gossen, M. & Bujard, H. Tight control of gene expression in mammalian cells by tetracycline responsive promoters. Proc. Natl. Acad. ScL USA 89:5547-5551(1992)); Urlinger, S., Baron, U., Thellmann, M., Hasan, M. T., Bujard, H. & Hillen, W. Exploring the sequence space for tetracycline- dependent transcriptional activators :Novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. USA 97(14):7963-7968(2000)).

Molecular Toggle Switch is another example of an inducible promoter. The toggle switch consists of a single plasmid LTRi and the ligand isopropyl-b- thiogalactopyranoside (IPTG). In the off state, the constitutively expressed Lad repressor binds to lac operator sites and blocks both RSV promoter-driven expression of the gene of interest and CMV -promoter-driven expression of the TetR repressor protein. Repression of TetR allows U6 promoter-dependent expression of a shRNA, which binds to a target sequence located in the 3' UTR of the gene of interest to further repress expression of the target gene. In the on state, IPTG binding to Lad inhibits Lad binding to its operator sites, thereby allowing the RSV promoter to drive expression of the gene of interest and the CMV promoter to drive expression of TetR. The TetR then binds to a Tet operator site in the U6 promoter to repress expression of the shRNA inhibitory component. (Deans, T. L., Cantor, C. R., and Collins, J.J. "A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells" Cell 130: 363-372(2007)).

Another example of an inducible promoter is the Q-mate Inducible Expression System (Q Biogene). The Q-mate inducible expression system is composed of the pCMV5-CymR and pCMV5 (CuO) plasmids and the ligand cumate. The pCMV5-CymR plasmid constitutively expresses the CymR protein from the CMV5 promoter. In the off state, CymR binds to its operator site in the pCMV5 (CuO) plasmids to repress transcription of the gene of interest from the CMV5 promoter. In the presence of cumate, CymR undergoes a conformational change and can no longer associate with its operator sequence. Promoter repression is then relieved and the CMV5 efficiently drives expression of the gene of interest. (See Mullick A, et al, "The cumate gene-switch: a system for regulated expression in mammalian cells," BMC Biotechnol 6:43 (2006). Another Example of an inducible promoter that can be used in the methods of the invention is the Argent Regulated Transcription Plasmid Kit (Ariad). The Argent Regulated Transcription Plasmid Kit includes the pC₄N₂-RπS3H/ZF3 and pZ12I-PL-2 plasmids and the ligand AP21967. The pC₄N₂-R_HS3H/ZF3 plasmid constitutively expresses the DNA binding domain fusion protein ZF3 and the activation domain fusion protein R_HS. ZF3 is a fusion of two zinc finger domains from Zif268, a homeodomain from Oct-1, and three copies of FKBP 12. R_HS is a fusion of a modified FRB fragment of FRAP and activation domains from the NF- kB p65 and heat shock protein 1. The pZ12I-PL-2 plasmid drives expression of the gene of interest from a minimal IL-2 promoter and 12 copies of ZF3 binding sites. In the absence of the ligand AP21967, ZF3 binds to its binding sites but is unable to activate transcription. In the on state, the ligand AP21967 forms a heterodimer between ZF3-FKBP12 domains and R_HS_FRAP domain. As a result, the R_HS activation domains are recruited to the promoter and transcription of the gene of interest proceeds. (Rivera, V. M., et al, "A humanized system for pharmacologic control of gene expression,'Wα/, Med., 2: 1028-32 (1996)).

As will be apparent to one of skill in the art, the biosensor polypeptide can comprise additional elements and such elements will depend on the interaction being assessed. For example the biosensor polypeptide can comprise regulatory elements (e.g., promoter, enhancers) in addition to the inducible promoter. Examples of such promoters include a heat shock protein promoter (HSP), a cmv promoter, (e.g., a modified cmv promoter) and the like. In certain aspects, the polypeptide is further operably linked to a minimal eukaryotic promoter, such as a heat shock promoter. Jn the case of a heat shock promoter, the activator is a physical activator.

The methods and reagents of the invention are typically performed or used in cells (e.g., living cells), such as vertebrate cells, including mammalian cells (e.g., human cells, rat cells, mouse cells, primate cells and the like), and invertebrate cells (e.g., insect cells and the like). Such cells can be primary cells, stem cells, immortalized cells, cell lines and the like. Diseased cells or genetically altered cells are also useful in the methods of the invention.

In one aspect, the cell comprises the endogenous polypeptide that interacts with the binding domain of the biosensor polypeptide. When the endogenous polypeptide occurs in the cell the choice of cell depends on the biosensor polypeptide and agent that are being assessed. For example, if the endogenous polypeptide is a cancer related polypeptide, and the agent being assessed is a drug candidate, the cell of choice would be a cancer cell that expresses the cancer related endogenous polypeptide. Alternatively, the methods of the invention can be performed using cells which do not normally express the endogenous protein, that is, the endogenous protein is introduced into a cell that does not express the protein along with the introduction of the biosensor polypeptide and agent. In this instance, the endogenous polypeptide is not an endogenous polypeptide in the true sense. However, it is the polypeptide that interacts with the binding domain of the biosensor polypeptide. For example, in tumor cells where the tumor suppressor p53 has been mutated or deleted, a wild type p53 molecule can be introduced into the cell that can then interact with a fluorescent protein biosensor component that has also been introduced into the same cells that have a binding domain complementary to the wild type p53. In another example, cells which already express the wild type stress kinase ERK at a certain level can be manipulated to express wither a higher or lower copy number of the enzyme. The fluorescent protein biosensor component expressed in the same cells will report on the activation of endogenously expressed ERK. Also provided are vectors, (e.g., expression vectors), comprising the nucleic acid sequences encoding one or more polypeptides of the invention. Vectors can be any construct suitable for bacterial, viral, insect, or mammalian propagation and/or expression, as known in the art. As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors {e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Expression vectors are capable of directing the expression of genes to which they are operably linked. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses) that serve equivalent functions. Host cells comprising such vectors are also provided by the present invention. It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed and the level of expression of polypeptide desired (See, for example, Ausubel, F. M. et al. , eds. Current Protocols in Molecular Biology, Greene Publishing Associates and John Wiley & Sons Inc. (1993).

Introduction of the biosensor polypeptide or an agent of interest to a cell can be by any suitable means. As used herein, "introduction to a cell" means both the " intracellular incorporation or uptake of the polypeptide and/or agent into the cell, or the extracellular exposure of a cell to an agent (e.g., a ligand that binds to a receptor on the surface of the cell such as a tyrosine kinase receptor ligand) as described herein. For example, introduction into a cell can be by transfection, electroporation, optoinjection, membrane translocating signal sequence attachment, cell scraping, detergent treatment of the cell, or other bulk-loading methods. Such methods are standard in the art. Extracellular exposure of a cell to an agent as described herein can be by adding the agent to the extracellular environment of the cell (e.g., cell culture medium).

The invention described herein provides methods for identifying an agent that modulates the interaction of the endogenous polypeptide and the biosensor polypeptide as described above. As used herein "modulates" refers to enhancing or inhibiting the interaction between a biosensor polypeptide and a endogenous polypeptide partially or completely. The agent can modulate the interaction of the biosensor polypeptide and the endogenous polypeptide either directly (e.g., completes for binding, sterically impedes binding and the like) or indirectly acts upstream or downstream) on molecules that are needed for the endogenous polypeptide to interact with the biosensor polypeptide. An (one or more) agent can be any test compound or molecule of interest, such as a drug. In one embodiment, the agent is one or more agents from a library of agents. In another embodiment, the library of agents is a library of macromolecules, small molecules or a combination thereof. As used herein, a small molecule is a small organic molecule of <1000 M. W. Macromolecules are molecules having a >1000 M. W. In one embodiment, a macromolecule is a protein, peptide, nucleic acid (e.g., DNA, RNA, PNA and/or aptamers), simple carbohydrate, complex carbohydrate, fatty acid, lipid molecule, or a combination thereof. Additionally, the agent is environmental such as treatment of the cells with radiation, heat, cold, light of various wavelengths, or other classes of electromagnetic radiation such as electricity, x-rays, or gamma rays.

The method further comprises introducing to the cell an agent, and detecting the cellular location of the biosensor polypeptide before and or after introduction of the agent to the cell. A change is location is determined by detecting the location of the reporter domain of the biosensor In one embodiment, the agent disrupts the interaction of polypeptides, thereby permitting the biosensor polypeptide to change its cellular location in the cell as determined by the localization domain.

In another embodiment, the cellular location of the biosensor polypeptide is detected after introduction of the agent. In another embodiment, the cellular location of the biosensor polypeptide id detected before and after introduction of the agent. In addition, the determination step can further comprise the use of any suitable control. For example, the cellular location of the biosensor polypeptide can be detected after (or before and after) introduction of the agent being assessed and the cellular location can be compared to the cellular location of a biosensor polypeptide (the same or similar biosensor polypeptide) present in a cell (the same or similar cell) which has not been exposed to the agent being assessed.

The detection can be in one step but is not necessary, the location of biosensor polypeptide bound to the endogenous polypeptide (first cellular location) can be known in advance and this is not necessary to detect. As described herein, after the agent is introduced to the cell the localization of the biosensor polypeptide to a second location is detected.

Determination of the cellular location of the biosensor polypeptide is performed in the presence of the agent. In another embodiment, detecting the cellular location of the biosensor polypeptide is performed after introduction and subsequent removal of the agent.

An agent, as described, above can be introduced to the cell and the cellular location of the biosensor polypeptide is determined, wherein a change in location indicates that the agent modulates the interaction of endogenous protein and the biosensor polypeptide. In one aspect, the change in location of the biosensor polypeptide is from a nuclear location to a cytoplasmic location. Alternatively, the change can be from the cytoplasm to the nucleous.

The method for identifying an agent that modulates the interaction of the endogenous polypeptide and the biosensor polypeptide comprises introducing to a cell a biosensor polypeptide and an agent. It will be apparent to one of skill in the art that one or more of the steps of the methods described herein can be performed sequentially or simultaneously. For example, the biosensor polypeptide can be added to the cell which comprises the endogenous polypeptide, then after a particular period of time, the agent can be added to the cell. Alternatively, the agent can be added first to the cell comprising the endogenous polypeptide and then after a particular period of time the biosensor polypeptide can be added to the cell. Each addition can be accomplished at together or simultaneously, or with a specified time. It will also be apparent to one of skill in the art that the particular interaction being assessed may require a specified sequence of order. Furthermore, varying the order and timing of each step may also provide useful insight regarding interaction and the role of the agent in the interaction between the binding domain and endogenous polypeptide.

The methods further comprise maintaining the cell under conditions in which the binding domain of the biosensor polypeptide interacts with the endogenous polypeptide in the cell, which results in localization of the biosensor polypeptide at a cellular location in a cell and disruption of the interaction may result in a change of location.

Conditions under which the cell is maintained so that the binding domain of the polypeptide interacts with the endogenous polypeptide most often is typical cell culture conditions as routinely used in the art.

The reagents of the invention include polypeptides, nucleic acid encoding polypeptides, comprising a binding domain, a localization domain and a reporter domain, all of which are operably linked to an inducible promoter. Also included in the invention are kits comprising the reagents of the invention. For example, a kit comprising, a vector comprising a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a binding domain, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter; a host cell comprising an endogenous polypeptide; and instructions for use.

The methods and reagents of the invention further provide for one or more multiplexed HCS assays that utilize flexible reagents, and combinations of reagents, to detect molecular interactions and their impact on cellular functions, and further to apply this detection of molecular interactions and impact on cell function to drug discovery research.

In one aspect of the invention, as detailed in Example 2 of the Exemplification, an ERK biosensor was expressed within mammalian cells. The ERK biosensor comprised a localization domain that directed the biosensor to the nucleus when it was not bound to activated ERK, an interaction domain that bound to activated ERK, and a reporter domain comprised of a green fluorescent protein. Furthermore, the nucleotide sequence encoding the ERK biosensor was under the transcriptional control of an inducible promoter to enable temporally regulated biosensor expression in living mammalian cells.

To demonstrate the function of the inducible ERK biosensor, human cells were nucleofected eith expression vectors comprising the ERK biosensor. The cells were treated with the activator, ponasterone A, to induce expression of the ERK biosensor. Activation (phosphorylation)of endogenous ERK in the cells was accomplished with thel2-O-tetradecanoylphorbol-13-acetate (TPA). The intracellular localization of the inducible ERK biosensor was assessed using standard fluorescence microscopy techniques. Cells were assessed in the presence and absence of the agent. In untreated cells, the inducible ERK biosensor was predominately localized in the nucleus. In treated cells, the inducible ERK biosensor was predominately localized in the cytoplasm,. This result is consistent with TPA induced ERK activation causing the net translocation of the inducible ERK biosensor from the nucleus to the cytoplasm. Quantification of biosensor translocation in a population of cells provided a readout of the ERK activation induced by TPA as well as other compounds. Furthermore, the limited exposure of the cells to the expression of the biosensor provided a large population of unperturbed cells for small or large scale ERK activation screens for compounds that modulate ERK activity.

In this Example, activated ERK bound to the polypeptide provided a steric hindrance of the NLS of the biosensor polypeptide that resulting in a shift in the localization from the dominant nuclear localization to a biased cytoplasmic localization. Because many different stimuli, including growth factors, cytokines, virus infection, ligands for heterotrimeric G protein-coupled receptors, transforming agents and carcinogens activate the ERK pathway, having an inducible promoter for careful monitoring of the expression of the binding domain allows for increased sensitivity and control over the conditions for experimentation. Thus, key regulatory pathways such as gene expression and signal transduction are minimally perturbed with the biosensor is only expressed in the cell during the time of experimentation and only at the level required to make measurements.

EXEMPLIFICA TION

Example 1 : Expression of Biosensor Components in cells

Optimizing the expression level of the p53-HDM2 PPIB produced large populations of qualified biosensing cells demonstrating that biosensor components can be temporally expressed in cells. In this example, a PPIB designed to quantify the p53-HDM2 interaction

(Giuliano, K. A., et al, (in press): Optimal characteristics of protein-protein interaction biosensors for cellular systems biology profiling. In High Content Screening: Science, Technology, and Applications. S.A. Haney, editor. Wiley, New York (2008)) into human lung carcinoma cells (A549) was delivered into a cell and the effects of the PPIB expression level on multiple cellular systems at 24 and 48 h after delivery were measured. In one case, A549 cells were transfected with an adenovirus encoding a fluorescent protein to define the optimal levels that produced measurable signals from the biosensor 24 h after infection that minimally altered cell function.

Human A549 lung carcinoma cells (CCL- 195) were obtained from the American Type Culture Collection (ATCC; Manassas, VA). Cells were cultured in complete McCoy's growth medium plus 10% fetal bovine serum and penicillin- streptomycin. For drug treatment, cells infected with adenoviruses expressing the two p53-HDM2 PPIB components (see below) were plated at a density of 5000 cells per well (40 μl) in 384-well microplates (Falcon #3962; Thermo Fisher) that were coated with collagen I. Cells were exposed to drugs 24 h after plating. Concentrated stocks of all drugs were diluted into solutions of HBSS plus 10% fetal bovine serum and added to the microplates (10 μl per well) using an automated liquid handling system (Biomek® 2000; Beckman-Coulter, Inc., Fullerton, CA).

p53-HDM2 PPIB construction and delivery into cells The basic construction of the p53-HDM2 PPIB has been described in detail

(Giuliano, K.A., et al, (in press): Optimal characteristics of protein-protein interaction biosensors for cellular systems biology profiling. In High Content Screening: Science, Technology, and Applications. S.A. Haney, editor. Wiley, New York (2008)). We used an adenoviral-based delivery system to express the biosensor in A549 cells. Recombinant adenoviruses for each component of the p53- HDM2 PPIB were constructed by inserting the expression cassettes of each of the biosensor components into the adenovirus genome in the El deletion site of the replication defective adenovirus genome. This was achieved using a standard recombinant adenovirus production method. In short, the p53 and hDM2 biosensor expression cassettes were inserted into a shuttle plasmid which was used to shuttle the expression cassette into the adenovirus genome. The highly specific endonucleases, I-Ceu I and PI-Sce I, were used to digest the shuttle plasmid and the adenoviral plasmid for in vitro ligation of the expression cassette to insert each of the two biosensor components into separate adenoviral plasmids. These were then screened for the recombinant adenovirus. Adenoviruses expressing each component of the biosensor were then produced in HEK-293 cells and stored at -80 C until needed.

To produce large populations of A549 cells expressing the two-component p53-HDM2 PPIB, 3 x 10⁶ cells were infected with both components of the biosensor at the levels described in the Results section for 1 h at 37 ⁰C in a total volume of 200 μl and then transferred to 384-well microplates as described above before treatment with compounds. At the end of an experiment, cells were fixed and analyzed as described previously (Giuliano, K.A., et al, (in press): Optimal characteristics of protein-protein interaction biosensors for cellular systems biology profiling. In High Content Screening: Science, Technology, and Applications. S.A. Haney, editor. Wiley, New York (2008)). The A549 cells were infected with a combination of two adenoviruses encoding the PPIB components (p53:HDM2 component ratio of 40:1) for only 24 h. In FIG. 1 , distribution maps show multiple cell population responses for cell cycle and nuclear morphology (Y-axis). Populations of cells were binned according to their expression level of the HDM2 PPIB component (X-axis). The other maps show measurements of cell health for cells in each of the PPIB expression bins. Under these conditions of adenoviral infection, the population of cells in which no PPIB expression could be detected was < 10% of the total population, in one third of the cell population (Sub Level). In the cells where PPIB expression was detected (Biosensing Levels), 80% of the population expressed the PPIB at a level that did not perturb the cells (Non-Manipulating Levels). The remaining fraction of the biosensing population (Manipulating Levels) expressed the PPIB at levels that induced small changes in the DNA content. If, on the other hand, expression of the biosensor was allowed to continue for an additional 24 h (e.g., 48 h after the initiation of biosensor expression), only 5 out of the 15 expression levels contained biosensor levels that minimally perturbed key cell activities (30% of the population). Thus, selecting the expression level and time of expression of the PPIB allowed reliable incorporation of the biosensor into a Cellular Systems Biology (CSB) profile that was used to build functional relationships between biomarker activities and the activities of compounds that modulated these relationships.

Example 2: A single polypeptide biosensor for stress kinase ERK activation whose expression is temporally regulated with an inducible promoter.

Protein kinases are promising targets for drug discovery and development. More than 1000 protein kinases have been identified, each one is a potential drug target. A key regulatory component of protein kinase pathways is the kinases' interaction with other cellular proteins. A fluorescent protein biosensor was designed to measure the activation of the stress kinase ERK. The biosensor polypeptide, a polypeptide expressed within mammalian cells, was comprised of a localization domain that directed the biosensor to the nucleus when it was not bound to activated ERK, an interaction domain that bound to activated ERK, and a reporter domain comprised of a green fluorescent protein. Furthermore, the nucleotide sequence encoding the ERK biosensor was under the transcriptional control of an inducible promoter to enable temporally regulated biosensor expression in living mammalian cells.

Specifically, the inducible ERK biosensor (pCLMN-259B) was comprised of an inducible promoter encoding a 5x E/GRE (Ecdysone / Gluocorticoid Receptor Element) sequence (FIG. 2, nucleotides 1-174); a eukaryotic heat shock protein (HSP) minimal promoter (FIG. 2 , nucleotides 181-475); the fluorescent protein reporter domain (FIG.2, nucleotides 498-1211), the nuclear localization domain (FIG. 2, nucleotides 1263-1427); and the ERK interaction or binding domain (FIG. 2, nucleotides 1485-1538). FIG. 3 shows a vector map of the inducible biosensor region within the biosensor expression vector.

Accessory proteins required for the inducible expression of the ERK biosensor were incorporated into a separate expression vector (FIG. 3; pERV3). The pERV3 vector was comprised of a cytomegalovirus (CMV) derived promoter (FIG. 3, complementary nucleotides 5201-5789) driving the expression of the modified ecdysone receptor (VgEcR) (FIGs. 4.1-4.2 complementary nucleotides 2912-5179) coupled with an internal ribosome entry site (IRES) (FIG. 4, complementary nucleotides 2332-2902) that was used to drive the expression of the RXR portion of the inducer ligand receptor (FIG. 4, complementary nucleotides 912-2216) in tandem with and SV40 poly A signal sequence (FIGs. 4.1 and 4.2: complementary nucleotides 463-901). FIG. 5 shows a map of the pERV3 expression vector. To demonstrate the function of the inducible ERK biosensor, 4 x 1O⁺⁶ U2OS human osteosarcoma cells (HTB-96; American Type Culture Collection, Manassas, VA) were nucleofected with a mix of 1.5 μg of the pCLMN-259A expression vector and 1.5 μg of the pERV3 expression vector using standard instrumentation and a protocol from Amaxa, Inc. (Gaithersburg, MD). The cells were then transferred to a T-25 tissue culture flask containing 5 ml complete growth medium and incubated for 5 h at 37⁰C in a humidified 5% CO₂ atmosphere. Cells were treated with 5.0 μM ponasterone A to induce expression of the ERK biosensor. After a 19 h incubation at 37⁰C, the cells were transferred to a 384-well microplate in the presence of 5.0 μM ponasterone A and incubated for an additional 5 h. To activate ERK, cells expressing the biosensor were treated with 1 μM 12-O-tetradecanoylphorbol-13- acetate (TPA) for 30 min at 37⁰C. The cells were then fixed with 3.7% formaldehyde in Hank's balanced salt solution (HBSS) for 30 min followed by rinsing in HBSS. The intracellular localization of the inducible ERK biosensor was assessed using standard fluorescence microscopy techniques. FIG. 6 shows example responses of cells expressing the inducible ERK biosensor to treatment with 1 μM TPA. In untreated cells (without TPA) FIG. 6, top row of images), the inducible ERK biosensor was predominately localized in the nucleus. In treated cells (FIG. 6, bottom row of images), the inducible ERK biosensor was predominately localized in the cytoplasm, consistent with TPA induced ERK activation causing the net translocation of the inducible ERK biosensor from the nucleus to the cytoplasm.

Quantification of biosensor translocation in a population of cells provided a readout of the ERK activation induced by TPA as well as other compounds. Furthermore, the limited exposure of the cells to the expression of the biosensor provided a large population of unperturbed cells for small or large scale ERK activation screens for compounds that modulate ERK activity.

FIG. 7 shows a inducible promoter referred to a gene switch attached to a biosensor polypeptide(or biosensor component) comprising JRED, which in turn is attached to NES/NLS, which in turn is attached to HDM2 (1-118), and that attached to pCLMN-237-D. This assemblage is in associative and/or interactive proximity to a gene switch attached to biosensor (or biosensor component) comprising p53(l- 131), which in turn is attached to REV(I -74), which in turn is attached to TagGFP, and that is attached to pCLM-237-E. A midi prep can be made available, the interaction can be tightly regulated, and the functionality can be assessed by assay.

FIG. 8 shows a biosensor polypeptide (with a gene switch) in the OFF position wherein a RheoReceptor-1 attached to Pl is proximate P2 attached to RheoActivator, with diverging arrows from Pl and P2 in the presence of pNEBR- Rl, the switch component (RheoReceptor- 1 ) proximate to the 5XRE within pNEBR-Xl does not enable the switch component RheoActivator to turn on the Gene-of-Interest. When the gene switch is switched ON by RSLl , the RheoReceptor component of the switch is activated by the RSLl and the RheoActivator associates with and activates a Basal Transcription Complex to turn ON the Gene-of-Interest. The switch can be utilized to manipulate the expression of key regulatory proteins, in both transient and stable expression. The expression can be optimized for different cell types, and the typical transfection efficiency can be approximately 50% in one embodiment. The expression is tightly regulated by the RSLl ligand, protein localization is normal, e.g., p53, hdm2 and p27 exhibit the expected predominate nuclear localization.

FIG. 9 shows photographic results of (a) cells for which an inducible promoter attached to a TagGFP, in turn attached to HDM2(FL); (b) cells for which an inducible promoter is attached to a TagGFP, in turn attached to a p53(FL); and (c) cells for which a Switch is attached to a TagGFP, in turn attached to a p27 polypeptide.

Another example of the invention includes a vector encoding a biosensor fusion protein having a fluorescent label, the RSK binding domain of ERK having nuclear localization and nuclear export sequences located near the RSK binding domain such that binding of ERK in living cells induces a change in the distribution of the biosensor upon activation of ERK. To control the expression of biosensor in living cells and, therefore, the possible modulating activity of the expression on cellular systems, the vector can also include a gene switch that controls the expression level of the biosensor fusion protein only when required.

FIG. 10 shows a Switch-ERK Biosensor method wherein an MK2NES(49 aa) component attached to NLS(7), which is in turn attached to an RSK(28aa) component, wherein the ERK associates with the RSK-NLS fragments to cause movement of the assemblage into the Cytoplasm when treated with TPA (/30 min). In the untreated control the same assemblage is located in the nucleus

Another preferred embodiment provides for a vector encoding a biosensor fusion protein having a fluorescent label, protease cleavage site or sites (e.g., caspase 3 cleavage site of DEVD), and a domain that keeps the fluorescent label localized in the cytoplasm until the cytoplasmic protease is activated. Activation of the cytoplasmic protease in living cells induces a change in the distribution of the biosensor such that the fluorescent label with its nuclear localization signal is free to distribute to the nucleus. -To control the expression of biosensor in living cells and, therefore, its possible modulating activity on cellular systems, the vector also includes a gene switch that controls the expression level of the biosensor fusion protein only when required.

FIG. 11 shows a Caspase-3 Biosensor, wherein a fluorescent protein (FP) component attached to NLS is associated and/or attached to 5xDEVD, which in turn is attached to Annexin II. Caspase 3 activation cleaves the 5xDEVD motif, causing translocation to the Nucleus. Prior to Caspase activation TagGFP-NLS-5xDEVD- Annexin II will be biased to the cytoplasm in HEK293T/mini-prep and similarly JRED-NLS-5xDEVD- Annexin II will be biased toward the cytoplasm in a U20S/midi-prep. The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.

While this invention has been particularly shown and described with references to example embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.

Claims

1. A method for identifying an agent that modulates the interaction between two polypeptides in a cell comprising, a) introducing into a cell that expresses an endogenous polypeptide, a biosensor comprising all or a portion of a binding domain that interacts with all or a portion of the endogenous protein, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter; b) introducing one or more activating molecules into the cell, wherein the activating molecule induces expression of the biosensor polypeptide in the cell; c) maintaining the cell under conditions in which the binding domain of the biosensor polypeptide interacts with the endogenous polypeptide, which results in localization of the biosensor polypeptide, to a cellular location; d) introducing an agent to the cell; and e) detecting the cellular location of the biosensor polypeptide, wherein a change in the cellular location of the biosensor polypeptide as compared to the cellular location in step b) indicates that the agent modulates the interaction between the biosensor polypeptide and the endogenous polypeptide.

2. The method of Claim 1, wherein the inducible promoter is a chemical based promoter.

3. The method of Claim 1, wherein the inducible promoter is an ecdysone based promoter.

4. The method of Claim 1, wherein the activating molecules comprises one or more accessory polypeptides present in a separate vector.

5. The method of Claim 1 , wherein the agent is a macromolecule, a small molecule, or a combination thereof.

6. The method of Claim 5, wherein the macromolecule is a protein, peptide, nucleic acid, aptamer, simple carbohydrate, complex carbohydrate, fatty acid, lipid molecule, or a combination thereof.

7. The method of Claim 1 , wherein the localization domain is selected from the group consisting of a nuclear localization domain, a nucleolar localization domain, a cytoplasmic localization domain, an organellar localization domain, and a combination thereof.

8. The method of Claim 1 , wherein the reporter domain is selected from the group consisting of: a fluorescent protein and a tag.

9. The method of Claim 8, wherein the tag is selected from the group consisting of a SNAP tag, a Halo tag, a Lumio, a FlAsH tag, and an epitope tag.

10. The method of Claim 1, wherein the biosensor polypeptide, the agent or a combination thereof is introduced into the cell by transfectioh, electroporation, optoinjection, membrane translocating signal sequence attachment, cell scraping, or detergent treatment of the cell.

11. The method of Claim 1 , wherein the endogenous polypeptide is selected from the group consisting of a disease-associated protein, a non-disease associated protein, and a combination thereof.

12. The method of Claim 1, wherein the disease-associated proteins are associated with cancer or neurodegenerative diseases.

13. The method of Claim 11 , wherein the non-disease associated protein is a metabolic pathway protein.

14. The method of Claim 1, wherein the endogenous polypeptide is a protein kinase.

15. The method of Claim 14, wherein the protein kinase is extracellular signal- regulated kinase, ERK.

16. The method of claim 1, wherein the biosensor polypeptide is encoded by a portion of SEQ ID NO: 1.

17. The method of Claim 4, wherein the accessory polypeptides are encoded by SEQ ID NO: 2.

18. A method for identifying an agent that modulates the interaction between extracellular signal-regulated kinase, ERK and a polypeptide that interacts with ERK, comprising: a) introducing into a cell that expresses ERK, the biosensor polypeptide and one or more activating molecules, wherein the activating molecules induces expression of the biosensor polypeptide in the cell; b) maintaining the cell under conditions in which the binding domain of the biosensor polypeptide interacts with ERK, which results in localization of the biosensor polypeptide to a cellular location; c) introducing an agent to the cell; and d) detecting the cellular location of the biosensor polypeptide, wherein a change in the cellular location of the biosensor polypeptide as compared to the cellular location in step b) indicates that the agent modulates the interaction of the biosensor polypeptide and ERK.

19. The method of Claim 18, wherein the biosensor polypeptide comprises all or a portion of a binding domain that interacts with all or a portion of the endogenous protein, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter.

20. The method of Claim 19, wherein the biosensor polypeptide is encoded by SEQ ID NO: 1.

21. The method of Claim 18, wherein the activating molecules comprise an activator.

22. The method of Claim 21 , wherein the activator is ponasterone A.

23. The method of Claim 18, wherein the activating molecules comprise accessory polypeptides.

24. The method of claim 23, wherein the accessory polypeptides are encoded by SEQ. ID NO: 3.

25. The method of Claim 18, wherein the agent is 12-O-tetradecanoylphorbol- 13-acetate (TPA).

• 26. A polypeptide comprising: a) at least a fragment of a polypeptide, wherein the fragment comprises a binding domain; b) a reporter domain; and c) a localization domain; wherein the binding domain, the reporter domain and the localization domain are all operably linked to an the inducible promoter.

27. A polypeptide encoded by SEQ ID NO. 1 (FIG. 2).

28. A vector comprising a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a binding domain, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter.

29. The vector of claim 28, comprising SEQ ID NO: 1.

30. A host cell comprising a vector, wherein the vector comprises a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a binding domain, a localization domain, and a reporter domain all of which are operably linked to an inducible promoter.

31. A kit comprising: a) a vector comprising a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a binding domain, a localization domain, and a reporter domain, all of which are operably linked to an inducible promoter; .b) a host cell comprising an endogenous polypeptide; and instructions for use.

32. The kit of Claim 31, wherein the nucleic acid sequence is SEQ ID NO: 1.