US 2011 0166330A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0166330 A1 Kobilka et al. (43) Pub. Date: Jul. 7, 2011

(54) GPCR CRYSTALIZATION METHOD USING (60) Provisional application No. 60/980,122, filed on Oct. AN ANTIBODY 15, 2007. (76) Inventors: Brian Kobilka, Palo Alto, CA Publication Classification (US); Daniel Rohrer, Los Gatos, CA (US); Peter Brams, (51) Int. Cl. Sacramento, CA (US); Asna C07K 6/00 (2006.01) Masood, Saratoga, CA (US) (52) U.S. Cl...... 530/387.3; 530/388.1 (21) Appl. No.: 12/931,528 (57) ABSTRACT (22) Filed: Feb. 2, 2011 An antibody that specifically binds a three dimensional Related U.S. Application Data epitope on the IC3 loop of a GPCR is provided. The antibody AV may be employed in a method that comprises: contacting a (62) Division of application No. 12/284.245, filed on Sep. GPCR with a monovalent version of the antibody binding 19, 2008, now Pat. No. 7,947,807. conditions to form a complex; and crystallizing the complex. Patent Application Publication Jul. 7, 2011 Sheet 1 of 8 US 2011/O166330 A1

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US 2011/0166330 A1 Jul. 7, 2011

GPCR CRYSTALIZATION METHOD USING of the IC3 loop of said GPCR is also provided. This method AN ANTIBODY may further comprise isolating a hybridoma line that pro duces the antibody. GOVERNMENT RIGHTS 0008. A method of making GPCR-containing vesicular antigens is also provided, as is a method of Screening hybri 0001. This work was supported in part by federal grant domas for the production of antibodies that bind to GPCR number NS28471 from the National Institutes of Health. The containing vesicles. federal government has certain rights in this invention. 0009. A method of using the antibody as a treatment for a GPCR-mediated disorder is also provided. BACKGROUND 0002 G protein-coupled (GPCR) signaling plays BRIEF DESCRIPTION OF THE FIGURES a vital role in a number of physiological contexts including, 0010. The patent or application file contains at least one but not limited to, metabolism, inflammation, neuronal func drawing executed in color. Copies of this patent or patent tion, and cardiovascular function. For instance, GPCRs application publication with color drawing(s) will be pro include receptors for biogenic amines, e.g., dopamine, epi vided by the Office upon request and payment of the neces nephrine, histamine, glutamate, acetylcholine, and ; sary fee. for purines such as ADP and ATP; for the vitamin niacin; for 0011 FIG. 1 is a schematic illustration of a GPCR, show lipid mediators of inflammation is such as prostaglandins, ing the canonical transmembrane regions (TM1, TM2, TM3. lipoxins, platelet activating factor, and leukotrienes; for pep TM4, TM5, TM6, and TM7), intracellular regions (IC1, IC2, tide hormones Such as calcitonin, follicle stimulating hor and IC3), and extracellular regions (EC1, EC2, and EC3). mone, gonadotropin releasing hormone, ghrelin, motilin, 0012 FIGS. 2A and 2B. Binding characteristics of BAR neurokinin, and oxytocin, for non-hormone peptides such as specific antibodies. 2A, Dot-blots showing binding of nine beta-endorphin, dynorphin A, Leu-enkephalin, and Met-en BAR specific antibodies to denatured receptor. Equal kephalin; for the non-peptide hormone melatonin; for amounts of BAR denatured with SDS and B-mercaptoetha polypeptides such as C5a anaphylatoxin and chemokines; for nol were spotted in triplicate on nitrocellulose strips. The proteases such as thrombin, trypsin, and factor Xa; and for strips were blocked with 5% non-fat dry milk in PBS-Tween sensory signal mediators, e.g., retinal photopigments and (0.05% Tween-20) and then probed with 1 mg/ml of the olfactory stimulatory molecules. GPCRs are of immense indicated antibodies diluted in blocking buffer. Binding of the interest for drug development. primary antibody to the denatured BAR was detected with an 0003. Efforts to crystallize GPCRs have been frustrated by Alexa-688 labeled anti-mouse secondary antibody. The top intrinsic characteristics of integral membrane proteins. panel is a graphical representation of the average dot intensity Bovine is the only GPCR for which a high-resolu from three independent experiments. The lower panel is a tion structure has been determined by X-ray crystallography; representative experiment. The binding of all 9 antibodies to and this is in part due to its natural abundance and atypical denatured fAR is reduced compared to M1 binding to the stability. The seven hydrophobic transmembrane helices of linear Flag epitope. 2B, Dose-response curves showing the GPCRs make poor surfaces for crystal contacts, and the extra effect on increasing amounts of is antibodies 4-9 on the fluo cellular and intracellular domains are often relatively short rescence of BAR labeled at C265 with tetramethyl and/or poorly structured. rhodamine (BAR-TMR). BAR-TMR was diluted to 4 nM in 500 uL of buffer consisting of 0.1% dodecylmaltoside, 100 SUMMARY OF THE INVENTION mM sodium chloride, and 20 mM HEPES buffer (pH 7.5). Data represent an in of 3. 0004 An antibody that specifically binds a three dimen (0013 FIGS. 3A and 3B. Fab 5 binds IC3 (labeled as IL3) sional epitope of the IC3 loop of a GPCR is provided. In of the BAR but does not effect structural changes associated certain embodiments, the antibody may specifically bind to with G protein activation. 3A, Western blot analysis of the the IC3 loop of the B2 adrenoreceptor. Also provided is a BAR digested with trypsin in the absence and presence of complex comprising a GPCR and a monovalent antibody that Fab 5. The fragmented fAR was visualized using an Alexa binds to a three dimensional epitope of the IC3 loop of that 680 labeled M1 antibody against the N-terminal Flag epitope. GPCR. The complex may be in a crystalline form. In the absence of Fab 5, two fragments at approximately 27 0005. A method is also provided. In general terms, the and 29 kDa appear corresponding to cleavage in the third method comprises: a) contacting a GPCR with a monovalent intracellular loop. In contrast, the presence of Fab 5 protects antibody that specifically binds to a three dimensional epitope the N-terminal end of the loop thus leaving the larger of the of the IC3 loop of a GPCR under binding conditions to form two fragments. The diagram shows the third intracellular loop a complex; and b) crystallizing the complex. In one embodi connecting TM5 and TM6. The loop is marked with MW ment, the GPCR comprises the B2ARIC3 loop, and the Fab indicators corresponding to N-terminal fragments containing fragment may bind to the B2AR IC3 loop. The GPCR may the Flag epitope. Residues sensitive to trypsin digest are also be a hybrid GPCR that contains the IC3 loop of B2AR. shown in red. 3B. The change in the bimane fluorescence of 0006. Also provided is a method comprising reconstitut BAR labeled with monobromobimane at H271C at the cyto ing a GPCR in artificial phospholipid vesicles to make an plasmic end of TM6. Bimane fluorescence is quenched by antigen; and immunizing an animal with the antigen. The W135 at the cytoplasmic end of TM3 upon agonist binding. animal may be a rabbit, mouse or chicken, for example. The response to the full agonist isoproterenol, isoproterenol 0007. A method comprising screening a plurality of hybri plus Fab 5, and Fab5 alone are shown. Fluorescence intensity doma lines obtained from an animal immunized with phos was corrected for background fluorescence from buffer and pholipid vesicles comprising a GPCR for a hybridoma that ligands in all experiments. The data are the mean+S.E. of two produces an antibody that bind to a three dimensional epitope independent experiments performed in triplicate. US 2011/0166330 A1 Jul. 7, 2011

0014 FIG. 4 Fluorescence images showing monoclonal nial, NY (1991) provide one of skill with general dictionaries antibody detection of flag tagged BAR stably expressed in of many of the terms used in this disclosure. Although any HEK-293 cells. HEK-293 cells stably expressing a flag methods and materials similar or equivalent to those tagged version of the BAR were cultured on coverslips and described herein can be used in the practice or testing of the processed for immunocytochemistry. After fixation, with 4% present invention, the preferred methods and materials are paraformaldehyde, the cells were washed and blocked with described. 2.5% goat serum in PBS alone (nonpermeabilized) or with 0020 All patents and publications, including all 0.5% NP-40 in PBS (permeabilized). The cells were incu sequences disclosed within Such patents and publications, bated with the BAR specific antibody indicated on the left referred to herein are expressly incorporated by reference. side of the figure. After several washes, the BAR monoclonal 0021 Numeric ranges are inclusive of the numbers defin antibodies were detected with a Texas Red conjugated anti ing the range. Unless otherwise indicated, nucleic acids are mouse secondary antibody. To demonstrate that all of the cells written left to right in 5' to 3' orientation; amino acid are expressing the receptor they were Subsequently stained sequences are written left to right in amino to carboxy orien with an Alexa-488 conjugated M1 antibody (M1 column), tation, respectively. which recognizes the amino terminal flag tag on the BAR. 0022. The headings provided herein are not limitations of Antibodies 1, 3, 4 and 8 stain cells in the absence of perme the various aspects or embodiments of the invention which abilization and therefore bind an epitope on the extracellular can be had by reference to the specification as a whole. face of the receptor. In contrast, antibodies 2, 5, 6, 7 and 9 only Accordingly, the terms defined immediately below are more stain cells that have been permeabilized indicative of an intra fully defined by reference to the specification as a whole. cellular epitope. The images shown are representative of at (0023 “G-protein coupled receptors', or “GPCRs” are least 3 experiments. All images were acquired using an polypeptides that share a common structural motif, having Axioplan 2 microscope (Carl Zeiss MicroImaging), fitted seven regions of between 22 to 24 hydrophobic amino acids with a camera (RTE/CCD-1300-Y/HS; Roper Scientific) that form to seven alpha helices, each of which spans a mem controlled using IPLab software (BD Bioscience). brane. As illustrated in FIG. 1, each span is identified by 0015 FIG. 5 Affinity of Fab 5 for purified BAR deter number, i.e., transmembrane-1 (TM1), transmembrane-2 mined by isothermal titration calorimetry (ITC). ITC mea (TM2), etc. The transmembrane helices are joined by regions surements were performed at 25°C. using a VP-ITC calorim of amino acids between transmembrane-2 and transmem eter (Microcal, Inc.). The ITC cell contained 11 uM brane-3, transmembrane-4 and transmembrane-5, and trans detergent-solubilized BAR or BAR buffer (blank titration), membrane-6 and transmembrane-7 on the exterior, or “extra and the injection syringe contained 70 uM Fab 5. Titrations cellular side, of the cell membrane, referred to as were initiated with a 3 ul injection, followed by a series of 8 “extracellular regions 1, 2 and 3 (EC1, EC2 and EC3), ul injections (37 BAR and 31 for BAR buffer blank), with respectively. The transmembrane helices are also joined by 240s between injections. After subtracting the blank titration, regions of amino acids between transmembrane-1 and trans the measured heat released upon binding was plotted against membrane-2, transmembrane-3 and transmembrane-4, and the Fab: BAR molar ratio, and the data were fitted to a transmembrane-5 and transmembrane-6 on the interior, or single-site binding model to obtain the association constant “intracellular side, of the cell membrane, referred to as Ka, enthalpy change AH, and stoichiometry n using the Ori “intracellular regions 1, 2 and 3 (IC1, IC2 and IC3), respec gin software package' (Microcal, Inc.) tively. The "carboxy” (“C”) terminus of the receptor lies in 0016 FIG. 6 Image of Fab 5-3 AR-TMR crystals. BAR the intracellular space within the cell, and the “amino” (“N”) was labeled with tetramethylrhodamine (BAR-TMR) and terminus of the receptor lies in the extracellular space outside mixed with an excess of Fab 5. The complex was purified by of the cell. GPCR structure and classification is generally well size exclusion chromatography. Crystals were grown in known in the art, and further discussion of GPCRs may be bicelles and ammonium sulfate (Rasmussen et al manu found in Probst, DNA Cell Biol. 1992 11:1-20; Marchese etal Script). Images were obtained by light (panel A) and fluores Genomics 23: 609-618, 1994; and the following books: Jür cence (panel B) microscopy. The fluorescence confirms the gen Wess (Ed) Structure-Function Analysis of G Protein presence offAR-TMR in the crystals. Bar represents 50 um. Coupled Receptors published by Wiley-Liss (1st edition; Oct. All images were acquired using an Axioplan 2 microscope 15, 1999); Kevin R. Lynch (Ed) Identification and Expression (Carl Zeiss MicroImaging), fitted with a camera (RTE/CCD of G Protein-Coupled Receptors published by John Wiley & 1300-Y/HS: Roper Scientific) controlled using IPLab soft Sons (March 1998) and Tatsuya Haga (Ed), G Protein ware (BD Bioscience). Coupled Receptors, published by CRC Press (Sep. 24, 1999); 0017 is FIG. 7 Figure illustrates packing of B2AR-Fab and Steve Watson (Ed) G-Protein Linked Receptor Facts complex in a crystal. book, published by Academic Press (1st edition: 1994). A 0018 FIG.8 Figure illustrates the B2AR-Fab complex. As schematic representation of an exemplary GPCR is shown in shown, the Fab5 antibody binds a three dimensional epitope FIG.1. A GPCR may be naturally occurring or non-naturally that contains amino acids from both ends of the IC3 loop. occurring (i.e., altered my man). 0024. The term “naturally-occurring in reference to a DEFINITIONS GPCR means a GPCR that is naturally produced (for example 0019. Unless defined otherwise herein, all technical and and not limitation, by a mammal or by a human). Such Scientific terms used herein have the same meaning as com GPCRs are found in nature. The term “non-naturally occur monly understood by one of ordinary skill in the art to which ring in reference to a GPCR means a GPCR that is not this invention belongs. Singleton, et al., DICTIONARY OF naturally-occurring. Wild-type GPCRs that have been made MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John constitutively active through mutation, and variants of natu Wiley and Sons, New York (1994), and Hale & Marham, THE rally-occurring GPCRs are examples of non-naturally occur HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Peren ring GPCRs. Non-naturally occurring GPCR may have an US 2011/0166330 A1 Jul. 7, 2011

amino acid sequence that is at least 80% identical to, e.g., at 0033. The term “fusion protein’ or grammatical equiva least 90% identical to, at least 95% identical to or at lest 99% lents thereof is meant a protein composed of a plurality of identical to, a naturally-occurring GPCR. polypeptide components, that while typically unjoined in 0025. The term “ligand’ means a molecule that specifi their native state, are joined by their respective amino and cally binds to a GPCR. A ligand may be, for example a carboxyl termini through a peptide linkage to form a single polypeptide, a lipid, a small molecule, an antibody. A "native continuous polypeptide. Fusion proteins may be a combina ligand is a ligand that is an endogenous, natural ligand for a tion of two, three or even four or more different proteins. The native GPCR. A ligand may be a GPCR “antagonist”, “ago term polypeptide includes fusion proteins, including, but not nist”, “partial agonist' or “inverse agonist', or the like. limited to, fusion proteins with a heterologous amino acid 0026. A “modulator is a ligand that increases or sequence, fusions with heterologous and homologous leader decreases a GPCR intracellular response when it is in contact sequences, with or without N-terminal methionine residues; with, e.g., binds, to a GPCR that is expressed in a cell. This immunologically tagged proteins; fusion proteins with term includes agonists, including partial agonists and inverse detectable fusion partners, e.g., fusion proteins including as a agonists, and antagonists. fusion partner a fluorescent protein, B-galactosidase, 0027. A "deletion' is defined as a change in either amino luciferase, etc.; and the like. acid or nucleotide sequence in which one or more amino acid 0034. The terms “nucleic acid molecule' and “polynucle or nucleotide residues, respectively, are absent as compared otide' are used interchangeably and refer to a polymeric form to an amino acid sequence or nucleotide sequence of a paren of nucleotides of any length, either deoxyribonucleotides or tal GPCR polypeptide or nucleic acid. In the context of a ribonucleotides, or analogs thereof. Polynucleotides may GPCR or a fragment thereof, a deletion can involve deletion have any three-dimensional structure, and may perform any of about 2, about 5, about 10, up to about 20, up to about 30 or function, known or unknown. Non-limiting examples of up to about 50 or more amino acids. A GPCR or a fragment polynucleotides include a gene, a gene fragment, exons, thereof may contain more than one deletion. introns, messenger RNA (mRNA), transfer RNA, ribosomal 0028. An “insertion' or “addition' is that change in an RNA, ribozymes, cDNA, recombinant polynucleotides, amino acid or nucleotide sequence which has resulted in the branched polynucleotides, plasmids, vectors, isolated DNA addition of one or more amino acid or nucleotide residues, of any sequence, control regions, isolated RNA of any respectively, as compared to an amino acid sequence or nucle sequence, nucleic acid probes, and primers. The nucleic acid otide sequence of a parental GPCR. “Insertion' generally molecule may be linear or circular. refers to addition to one or more amino acid residues within 0035. As used herein the term "isolated, when used in the an amino acid sequence of a polypeptide, while “addition” context of an isolated compound, refers to a compound of can be an insertion or refer to amino acid residues added at an interest that is in an environment different from that in which N- or C-terminus, or both termini. In the context of a GPCR the compound naturally occurs. “Isolated' is meant to include or fragment thereof, an insertion or addition is usually of compounds that are within Samples that are substantially about 1, about 3, about 5, about 10, up to about 20, up to about enriched for the compound of interest and/or in which the 30 or up to about 50 or more amino acids. A GPCR or compound of interest is partially or substantially purified. fragment thereof may contain more than one insertion. 0036. As used herein, the term “substantially pure” refers 0029. A “substitution results from the replacement of one to a compound that is removed from its natural environment or more amino acids or nucleotides by different amino acids and is at least 60% free, at least 75% free, or at least 90% free or nucleotides, respectively as compared to an amino acid from other components with which it is naturally associated. sequence or nucleotide sequence of a parental GPCR or a 0037 A“coding sequence' or a sequence that “encodes' a fragment thereof. It is understood that a GPCR or a fragment selected polypeptide, is a nucleic acid molecule which can be thereof may have conservative amino acid substitutions transcribed (in the case of DNA) and translated (in the case of which have substantially no effect on GPCR activity. By mRNA) into a polypeptide, for example, in a host cell when conservative substitutions is intended combinations such as placed under the control of appropriate regulatory sequences gly, ala; Val, ile, leu; asp. glu; asn, gln, ser, thr; lys, arg; and (or “control elements'). The boundaries of the coding phe, tyr. sequence are typically determined by a start codon at the 5' 0030 The term “biologically active', with respect to a (amino) terminus and a translation stop codon at the 3' (car GPCR, refers to a GPCR having a biochemical function (e.g., boxy) terminus. A coding sequence can include, but is not a binding function, a signal transduction function, or an abil limited to, cDNA from viral, procaryotic or eucaryotic ity to change conformation as a result of ligand binding) of a mRNA, genomic DNA sequences from viral or prokaryotic naturally occurring GPCR. DNA, and synthetic DNA sequences. A transcription termi 0031. As used herein, the terms “determining.” “measur nation sequence may be located 3' to the coding sequence. ing.” “assessing, and “assaying are used interchangeably Other “control elements’ may also be associated with a cod and include both quantitative and qualitative determinations. ing sequence. A DNA sequence encoding a polypeptide can Reference to an “amount of a GPCR in these contexts is not be optimized for expression in a selected cell by using the intended to require quantitative assessment, and may be codons preferred by the selected cell to represent the DNA either qualitative or quantitative, unless specifically indicated copy of the desired polypeptide coding sequence. otherwise. 0038 “Operably linked’ refers to an arrangement of ele 0032. The terms “polypeptide' and “protein', used inter ments wherein the components so described are configured so changeably herein, refer to a polymeric form of amino acids as to perform their usual function. In the case of a promoter, of any length, which can include coded and non-coded amino a promoter that is operably linked to a coding sequence will acids, chemically or biochemically modified or derivatized effect the expression of a coding sequence. The promoter or amino acids, and polypeptides having modified peptide back other control elements need not be contiguous with the cod bones. ing sequence, so long as they function to direct the expression US 2011/0166330 A1 Jul. 7, 2011 thereof. For example, intervening untranslated yet tran generally, Hood et al., “Immunology’, Benjamin, N.Y., 2nd scribed sequences can be present between the promoter ed. (1984), and Hunkapiller and Hood, Nature, 323, 15-16 sequence and the coding sequence and the promoter sequence (1986)). This term also encompasses so-called “phage dis can still be considered “operably linked to the coding play' antibodies. Sequence. 0046. A "monovalent antibody is an antibody that has a 0039. By “nucleic acid construct it is meant a nucleic acid single antigen binding region. Fab fragments, ScPV antibod sequence that has been constructed to comprise one or more ies, and phage display antibodies are types of monovalent functional units not found together in nature. Examples antibodies, although others are known. A “Fab' fragment of include circular, linear, double-stranded, extrachromosomal an antibody has a single binding region, and may be made by DNA molecules (plasmids), cosmids (plasmids containing papain digestion of a full length monoclonal antibody. A COS sequences from lambda phage), viral genomes compris single chain variable (or “scFv') fragment of an antibody is ing non-native nucleic acid sequences, and the like. an antibody fragment containing the variable regions of the 0040 A“vector is capable of transferring gene sequences heavy and light chains of immunoglobulins, linked together to a host cell. Typically, “vector construct.” “expression vec with a short flexible linker. tor, and "gene transfer vector” mean any nucleic acid con 0047. A “hybridoma' is a cell that is a hybrid of a spleen struct capable of directing the expression of a gene of interest cell or other antibody producing cell and an immortal cell and which can transfer gene sequences to host cells, which (e.g., a myeloma cell). Hybridomas are both immortal and can be accomplished by genomic integration of all or a por capable of producing the genetically coded antibody. Hybri tion of the vector, or transient or inheritable maintenance of domas and methodologies for making hybridomas may be the vector as an extrachromosomal element. Thus, the term found in U.S. Pat. No. 6,420,140 and Harlow, (Antibodies. A includes cloning, and expression vehicles, as well as integrat Laboratory Manual, First Edition (1988) Cold Spring Har ing vectors. bor, N.Y.) for example. 0041 An "expression cassette' comprises any nucleic 0048. A “complex” between an antibody an antigen is acid construct capable of directing the expression of a gene/ characterized by a K (dissociation constant) of less than coding sequence of interest, which is operably linked to a 10 M, less than 107M, less than 10 M, less than 10 M, promoter of the expression cassette. Such cassettes can be or less than 10 M. constructed into a “vector.” “vector construct.” “expression vector” or “gene transfer vector in order to transfer the 0049. The “IC3 loop” of a GPCR is the intracellular loop expression cassette into a host cell. Thus, the term includes that is between transmembrane region 5 (TM5) and trans cloning and expression vehicles, as well as viral vectors. membrane region 6 (TM6) of the GPCR. Such regions are 0042. A first polynucleotide is "derived from or “corre readily identifiable by analysis of the primary amino acid sponds to a second polynucleotide if it has the same or sequence of a GPCR. Substantially the same nucleotide sequence as a region of the 0050. The terms “specifically binds” and “specific bind second polynucleotide, its cDNA, complements thereof, or if ing refer to the ability of an antibody to preferentially bind to it displays sequence identity as described above. a particular antigen that is present in a homogeneous mixture 0043. A first polypeptide is “derived from' or “corre of different antigens. In certain embodiments, a specific bind sponds to a second polypeptide if it is (i) encoded by a first ing interaction will discriminate between desirable and unde polynucleotide derived from a second polynucleotide, or (ii) sirable antigens in a sample, in Some embodiments more than displays sequence identity to the second polypeptides as about 10 to 100-fold or more (e.g., more than about 1000- or described above. 10,000-fold). 0044) The terms “antibodies' and “immunoglobulin' 0051. An antibody that specifically binds to a “three include antibodies or immunoglobulins of any isotype, frag dimensional epitope or “conformational epitope is an anti ments of antibodies which retain specific binding to antigen, body that specifically binds to a tertiary (i.e., three dimen including, but not limited to, Fab, Fv, scFv, and Fd fragments, sional) structure a folded protein. Such an antibody binds at chimeric antibodies, humanized antibodies, single-chain much reduced (i.e., by a factor of at least 2, 5, 10, 50 or 100) antibodies, and fusion proteins comprising an antigen-bind affinity to the linear (i.e., unfolded, denatured) form of the ing portion of an antibody and a non-antibody protein. The protein. The structure to which such an antibody binds con antibodies may be detectably labeled, e.g., with a radioiso tains amino acids that are discontiguous in the protein. In tope, an enzyme which generates a detectable product, a other words, binding of Such an antibody to a polypeptide is fluorescent protein, and the like. The antibodies may be fur dependent upon the polypeptide being folded into a particular ther conjugated to other moieties, such as members of specific three dimensional conformation. binding pairs, e.g., biotin (member of biotin-avidin specific binding pair), and the like. The antibodies may also be bound DETAILED DESCRIPTION OF EXEMPLARY to a solid Support, including, but not limited to, polystyrene EMBODIMENTS plates or beads, and the like. Also encompassed by the terms are Fab'. Fv, F(ab'), and or other antibody fragments that 0052. As noted above, various compositions are provided, retain specific binding to antigen. including an antibody that specifically binds to a three dimen 0045 Antibodies may exist in a variety of other forms sional epitope of the IC3 loop of a GPCR, a complex contain including, for example, Fv, Fab, and (Fab'), as well as bi ing a monovalent fragment of the antibody and a GPCR, and functional (i.e. bi-specific) hybrid antibodies (e.g., Lanzavec a crystal containing the complex. Various crystallization chia et al., Eur. J. Immunol. 17, 105 (1987)) and in single methods are also provided. In particular embodiments, the chains (e.g., Huston et al., Proc. Natl. Acad. Sci. U.S.A., 85, GPCR to be complexed with the antibody may contain the 5879-5883 (1988) and Bird et al., Science, 242, 423-426 B2AR IC3 loop, and, in certain embodiments, may be a (1988), which are incorporated herein by reference). (See, hybrid GPCR that contains the IC3 loop of B2AR. Methods of US 2011/0166330 A1 Jul. 7, 2011 preparing an antigen, and screening for an antibody are also hybridoma cells may be screened, and positive clones are provided. These embodiments are described in greater detail expanded according to standard procedures (Harlow et al. below. Antibodies: A Laboratory Manual, First Edition (1988) Cold 0053 Antibodies spring Harbor, N.Y.; and Spieker-Polet et al., supra). 0054. A monoclonal antibody that that specifically binds 0059. The antibodies may be screened for binding to the to a three dimensional epitope of the IC3 loop of a GPCR is GPCR folded into a native conformation by, e.g., cell staining provided. Such antibodies may be made, in general terms, by to identify those antibodies that bind a three dimensional reconstituting an active GPCR in phospholipid vesicles, epitope in the GPCR. In certain cases, the antibodies may also immunizing a suitable animal with the phospholipid vesicles, be screened for binding to denatured GPCR. Antibodies that and Screening antibody-producing cells of the animal (or bind to the IC3 loop of the polypeptide may be identified hybridomas thereof) for the antibody. using any of a variety of different means, depending on the 0055 A GPCR may be produced and purified using con GPCR. For example, the antibody can be tested to determine ventional methods that may employ expressing a recombi if it can block interactions with a G-protein, or it can be tested nant form of the GPCR in a host cell, and purifying the GPCR on a GPCR containing amino acid substitutions in the IC3 using affinity chromatography and/or antibody-based meth loop. Other methods are described in the examples section of ods. In particular embodiments, the bactulovirus/Sf-9 system this disclosure. may be employed for expression, although other expression 0060. In alternative embodiments, a phage display anti systems (e.g., bacterial, yeast or mammalian cell systems) body may be employed, methods for the production of which may also be used. Exemplary methods for expressing and are well known (see, e.g., Scott et al. Science 1990 249: 386; purifying GCPRs are described in, for example, Kobilka Devlin et al., Science 1990 249: 404: U.S. Pat. Nos. 5,223, (Anal Biochem 1995 231,269-71), Eroglu etal (EMBO 2002 409, 5,733,731, 5,498,530, 5,432,018, 5,338,665, and 5,922, 3: 491–496), Chelikani et al (Protein Sci. 2006 15:1433-40) 545, for example). and the book “Identification and Expression of G Protein 0061 Any known GPCR is suitable for use in the subject Coupled Receptors' (Kevin R. Lynch (Editor), Wiley-Liss methods. A disclosure of the sequences and phylogenetic (March 1998)), among many others. relationships between 277 GPCRs is provided in Joost et al. 0056. Likewise, methods for reconstituting an active (Genome Biol. 20023:RESEARCH0063, the entire contents GPCR in phospholipid vesicles are known, and are described of which is incorporated by reference) and, as Such, at least in: Luca et al (Proc. Natl. Acad. Sci. 2003 100:10706-11): 277 GPCRs are suitable for the subject methods. A more Mansoor et al (Proc. Natl. Acad. Sci. 2006 103: 3060-3065); recent disclosure of the sequences and phylogenetic relation Niu et al. (Biophys J. 2005 89: 1833-1840); Shimada et al (J. ships between 367 human and 392 mouse GPCRs is provided Biol. Chem. 2002 277:31774-80); and Eroglu et al. (Proc. in Vassilatis et al. (Proc Natl Acad Sci 2003 100:4903-8 and Natl. Acad. Sci. 2003 100: 10219-10224), among others. In www.primalinc.com, each of which is hereby incorporated certain cases, the GPCR and phospholipids may be reconsti by reference in its entirety) and, as such, at least 367 human tuted at high density (e.g., 1 mg receptor per mg of phospho and at least 392 mouse GPCRs are suitable for the subject lipid). In particular embodiments, the phospholipids vesicles methods. GPCR families are also described in Fredriksson et may be tested to confirm that the GPCR is active. In many al (Mol. Pharmacol. 2003 63, 1256-72). Since the amino acid cases, a GPCR may be present in the phospholipid vesicle in sequences of many GPCRs are available and their code both orientations (in the normal orientation, and in the sequences are known, the Subject antibody may be made for “upside down' orientation in which the intracellular loops are any GPCR. For example, a human, mouse, rat, insect or plant on the outside of the vesicle). GPCR may be used in the subject method. 0057. Any suitable animal, e.g., a warm-blooded animal, 0062. The methods may be used, by way of exemplifica in particular a mammal such as a rabbit, mouse, rat, camel, tion, for purinergic receptors, vitamin receptors, lipid recep sheep, cow or pig or a bird such as a chicken or turkey, may be tors, peptide hormone receptors, non-hormone peptide recep immunized with the reconstituted GPCR using any of the tors, non-peptide hormone receptors, polypeptide receptors, techniques well known in the art Suitable for generating an protease receptors, receptors for sensory signal mediator, and immune response. Procedures for immunizing animals are receptors not including B2-adrenergic recep well known in the art, and are described in Harlow (Antibod tor. In certain embodiments, said biogenic amine receptor ies: A Laboratory Manual, First Edition (1988) Cold Spring does not include an adrenoreceptor. C-type adrenoreceptors Harbor, N.Y.) and Weir (Handbook of Experimental Immu (e.g. C. C. or Cadrenoreceptors) and f-type adrenore nology Vol 4, Blackwell Scientific Publishers, Oxford, ceptors (e.g. f. B., or f3. adrenoreceptors) are discussed in England, 1986). As will be appreciated by one of ordinary Singh et al., J. Cell Phys. 189:257-265, 2001. skill in the art, the immunogen may be admixed with an 0063. It is recognized that both naturally occurring and adjuvant or hapten in order to increase the immune response altered native (non-naturally occurring) GPCRs may be used (for example, complete or incomplete Freund's or lipid A in the Subject methods. In certain embodiments, therefore, an adjuvant), or with a carrier Such as keyhole limpet hemocya altered native GPCR (e.g. a native GPCR that is altered by an nin (KLH). amino acid Substitution, deletion and/or insertion) such that it 0.058. Once a suitable animal has been immunized and an binds the same ligand as a corresponding native GPCR may immune response against the antigen has been established by be used in the subject methods. the animal, antibody producing cells from the animal are 0064. As such, the following GPCRs (native or altered) screened to identify cells that produce antibodies having a find particular use as parental GPCRs in the subject methods: desired activity. In many embodiments, these methods may cholinergic receptor, muscarinic 3; melanin-concentrating employ hybridoma technology in which cells from the spleen hormone receptor 2; cholinergic receptor, muscarinic 4: nia of the immunized animal are fused with a suitable immortal cin receptor, histamine 4 receptor; ghrelin receptor, CXCR3 cell to produce hybridoma cells. Supernatants from these , ; 5-hydroxytryptamine US 2011/0166330 A1 Jul. 7, 2011

(serotonin) receptor 2A, 5-hydroxytryptamine (serotonin) Struct. Biol. 2003 142: 108-32. In general terms, the methods receptor 2B: 5-hydroxytryptamine (serotonin) receptor 2C: are lipid-based methods that include adding lipid to the fusion D3; , dopamine protein prior to crystallization. Such methods have previously receptor D1; H2; histamine receptor H3; been used to crystallize other membrane proteins. Many of 1; Y1; angiotensin these methods including the exploit the spontaneous self II receptor 1; 1; , assembling properties of lipids and detergent as vesicles glucagon-like peptide 1 receptor, ; can (vesicle-fusion method), discoidal micelles (bicelle method), nabinoid receptor 1; and melanin-concentrating hormone and liquid crystals or mesophases (in meso or cubic-phase receptor 1. method). Lipidic cubic phases crystallization methods are 0065. In certain embodiments, the antibody is a monova described in, for example: Landau et al. Lipidic cubic phases. lent antibody that contains a single antigen binding region a novel concept for the crystallization of membrane proteins. comprising variable heavy and variable light domains. Such Proc. Natl. Acad. Sci. 1996 93:14532-5; Gouaux, It's not just antibodies, including Fab antibodies and schv antibodies, a phase: crystallization and X-ray structure determination of may be produced from a monoclonal antibody after it is bacteriorhodopsin in lipidic cubic phases. Structure. 1998 identified. In one embodiment, the monovalent antibody is an 6:5-10; Rummel et al. Lipidic Cubic Phases. New Matrices antibody containing the heavy and light variable regions from for the Three-Dimensional Crystallization of Membrane Pro antibody 5, which is described in the examples section of this teins.J. Struct. Biol. 1998 121:82–91; and Nollert etal Lipidic disclosure. Suchantibodies include Fab fragment of antibody cubic phases as matrices for membrane protein crystalliza 5 (i.e., the Fab5 antibody) or a schv antibody comprising the tion Methods. 2004 34:348-53, which publications are incor same variable domains as the Fab5 antibody, where the heavy porated by reference for disclosure of those methods. Bicelle and light variable domains of the Fab5 antibody have the crystallization methods are described in, for example: Faham following amino acid sequence: etal Crystallization of bacteriorhodopsin from bicelle formu lations at room temperature. Protein Sci. 2005 14:836-40. 2005 and Faham et al. Bicelle crystallization: a new method Fab5 Light Chain: for crystallizing membrane proteins yields a monomeric bac (SEQ ID NO: 1) teriorhodopsin structure. J Mol Biol. 2002 Feb. 8; 316(1):1- DIKMTOSPSSMYASLGERVTITCKASODINSYLSWFOOKPGKSPKTLI 6, each of which are incorporated by reference for disclosure YRANRLVDGVPSRFIGTGSGODYSLITSSLDYEDMGIYYCLOYDEFPY of those methods. (0071. Also provided is a method of determining a crystal TFGGGTKLEIKRADAAPTVSIFPPSSEOLTSGGASVWCFLNNFYPKDI structure. This method may so comprise receiving an above NVKWKIDGSERONGVLNSWTDODSKDSTYSMSSTLTLTKDEYERHNSY described complex, crystallizing the complex to produce a crystal, and obtaining atomic coordinates of the GPCR from TCEATHKTSTSPIVKSFNRNEC the crystal. The complex may be received from a remote Fab5 Heavy chain: location (e.g., a different laboratory in the same building or (SEQ ID NO: 2) campus, or from a different campus or city), and, in certain EVOLOOSGAELARPGASVKLSCKASGYIFTDYYINWVRORTGOGFEWI embodiments, the method may also comprise transmitting the atomic coordinates, e.g., by mail, e-mailor, using the internet, GEIYPGSGNIDYNERFKDKATLTADKSSSTAYMOLSSLTSEDSAVYFC to the remote location or to a third party. WRGFGYWGOGTTLTVSSAKTTPPSVYPLAPGSAAOTNSMVTLGCLVKG 0072. In other embodiments, the method may comprise forwarding a complex to a remote location, where the com YFPEPVTVTWNSGSLSSGVHTFPAVLOSDLYTLSSSVTVPSSTWPSET plex may be crystallized and analyzed, and receiving the WTCNWAHPASSTKWDKKIWPRDCGC atomic coordinates of the GPCR. (0073. In certain cases, the GPCR to be crystallized may be 0066. In certain cases, a subject antibody may contain: a) a GPCR that has been modified to containa three dimensional a heavy chain containing the CDR1, CDR2 and CDR3 epitope from the IC3 loop from a different GPCR (e.g., the B2 regions of the heavy chain of an above-described antibody, GPCR). In these embodiments, once a suitable antibody has separated by framework sequence and b) a light chain con been identified for a first GPCR, the antigen binding region taining the CDR1, CDR2 and CDR3 regions of the light chain for that antibody can be swapped from the first GPCR into a of that antibody, separated by framework sequence. second GPCR to make a chimeric GPCR. The chimeric 0067. Also provided is a complex containing the GPCR GPCR can then be bound to a monovalent antibody, and and a single antigen binding region of the antibody. Such a crystallized using a method described herein. In one embodi complex may be formed under antibody binding conditions ment, the entire IC3 loop, including the three dimensional described in Harlow and Weir, supra. A crystal of the complex epitope contained in the loop, may be grafted from one GPCR is also provided, and methods of making of which are to another to produce an active GPCR. Such methods have described in greater detail below. been successfully performed by others, e.g., Kim et al (Bio 0068 Crystallization Methods chemistry 2005 44:2284-92): Yamashita etal (J. Biol. Chem. 0069. A crystallization method is also provided. The 2000 275:34272-9); Geiser et at (Protein Sci. 2006 15:1679 method includes contacting a GPCR with a monovalent anti 90); Tumova et al (J. Biol. Chem. 2003 278:8146-53); Wong body that specifically binds to a three dimensional epitope of etal (J. Biol. Chem. 1990 265:6219–24) and Wessetal (FEBS the IC3 loop of a GPCR under binding conditions to form a Lett. 1989 258:133-6). complex; and crystallizing the complex. (0074 The IC3 region of a GPCR lies in between trans 0070 A subject complex may be crystallized using any of membrane regions TM5 and TM6 and, may be about 12 a variety of crystallization methods, many of which are amino acids (CXCR3 and GPR40) to about 235 amino acids reviewed in Caffrey Membrane protein crystallization. J. (cholinergic receptor, muscarinic 3) in length, for example. US 2011/0166330 A1 Jul. 7, 2011

The TM5, IC3, and TM6 regions are readily discernable by position, to produce a chimeric GPCR. That chimeric GPCR one of skill in the art using, for example, a program for may be complexed with a monovalent version of antibody 5 identifying transmembrane regions; once transmembrane (e.g., a Fab fragment of antibody 5 or a schv antibody) to regions TM5 and TM6 regions are identified, the IC3 region make a complex that can be crystallized. In certain embodi will be apparent. The TM5, IC3, and TM6 regions may also be ments, the antibody 5 binding site sequences may be trans identified using such methods as pairwise or multiple ferred along with amino acids that flank the binding site (e.g., sequence alignment (e.g. using the GAP or BESTFIT of the up to 2, 3, 4, or 5 amino acids from each side). In particular University of Wisconsin's GCG program, or CLUSTAL embodiments, the entire IC3 region of the non-B2AR GPCR alignment programs, Higgins et al., Gene. 1988 73:237-44), may be substituted with the IC3 region of PAR. In certain using a target GPCR and, for example, GPCRs of known cases, the transferred may contain I233 to K270 of B2AR Structure. GPCR, and may contain amino acids that flank that sequence 0075 Suitable programs for identifying transmembrane (e.g., up to 2, 3, 4, or 5 amino acids from each side). In other regions include those described by Moller et al., (Bioinfor cases, two regions may be transferred, one containing the matics, 17:646-653, 2001). A particularly suitable program is amino acid sequence of I233 to V242, and the other contain called “TMHMM Kroghet al., (Journal of Molecular Biol ing the amino acid sequence of L266 to K270. These ogy, 305:567-580, 2001). To use these programs via a user sequences can be transferred to the N-terminus and the C-ter interface, a sequence corresponding to a GPCR or a fragment minus of the recipient GPCR's IC3, respectively. thereof is entered into the user interface and the program run. I0082. Thus, a chimeric GPCR used in the method may Such programs are currently available over the world wide containa) an IC3 loop of one GPCR (e.g., the B2 GPCR), and web, for example at the website of the Center for Biological b) TM1-TM7, IC1 and IC2 regions of another GPCR. Sequence Analysis at cbs.dtu.dk/services/. The output of 0083 Methods of Treatment these programs may be variable in terms its format, however I0084 Certain of the above-described antibodies may have they usually indicate transmembrane regions of a GPCR therapeutic utility and may be administered to a Subject hav using amino acid coordinates of a GPCR. ing a condition in order to treat the Subject for the condition. 0076. When TM regions of a GPCR polypeptide are deter The therapeutic utility for an antibody may be determined by mined using TMHMM, the prototypical GPCR profile is usu the GPCR to which the antibody binds in that signaling via ally obtained: an N-terminus that is extracellular, followed by that GPCR is linked to the condition. In certain cases, the a segment comprising seven TM regions, and further fol GPCR may be activated in the condition via by binding by a lowed by a C-terminus that is intracellular. TM numbering for ligand. In other embodiments, the GPCR may be mutated to this prototypical GPCR profile begins with the most N-ter make it constitutively active, for example. A subject antibody minally disposed TM region (TM1) and concludes with the may be employed for the treatment of a GPCR-mediated most C-terminally disposed TM region (TM7). condition Such as Schizophrenia, migraine headache, reflux, 0077 Accordingly, in certain embodiments, the amino asthma, bronchospasm, prostatic hypertrophy, ulcers, epi acid coordinates of the TM5, IC-3, and TM6 regions of a lepsy, angina, allergy, rhinitis, cancer e.g. prostate cancer, GPCR are identified by a suitable method such as TMHMM. glaucoma and stroke. Further exemplary GPCR-related con 0078. In certain cases, once the TM5-IC3-TM6 segment is ditions at the On-line Mendelian Inheritance in Man database identified for a GPCR, a suitable region of amino acids is found at the world wide website of the NCBI. chosen for Substitution with the amino acid sequence of an 0085. In certain embodiments as noted above, the anti IC3 region of another GPCR, e.g. the B2 GPCR. In certain body may bind to the B2-adrenoreceptor, in which case it may embodiments, the Substituted region may be identified using be employed in the treatment of a condition requiring relax conserved or semi-conserved amino acids in the TM5 and ation of smooth muscle of the uterus or vascular system. Such TM6 transmembrane regions. an antibody may be thus used for the prevention oralleviation 0079. For GPCRs that contain no conserved proline resi of premature labour pains in pregnancy, or in the treatment of dues in TM5 and TM6, positions for inserting a different IC3 chronic or acute asthma, urticaria, psoriasis, rhinitis, allergic loop may be based on two considerations: a) alignment of the conjunctivitis, actinitis, hay fever, or mastocytosis, which sequence of the GPCR with receptor members of the same conditions have been linked to the B2-adrenoreceptor. In subfamily (which contained conserved proline residues in these embodiments, the antibody may be employed as co TM5 or TM6; b) by identifying the juxtaposition to the TM5/ therapeutic agents for use in combination with other drug TM6 regions by hydrophobicity analysis. Substances such as anti-inflammatory, bronchodilatory or 0080. In addition to substituting IC3 region of a GPCR antihistamine drug Substances, particularly in the treatment with a stable, folded protein insertion, as described above, in of obstructive or inflammatory airways diseases such as those certain cases, the C-terminal region of the GPCR (which is mentioned hereinbefore, for example as potentiators of thera C-terminal to the cysteine palmitoylation site that is approxi peutic activity of Such drugs or as a means of reducing mately 10 to 25 amino acid residues downstream of a con required dosaging or potential side effects of Such drugs. A served NPXXY motif), may be deleted. In certain cases, the subject antibody may be mixed with the other drug substance 20-30 amino acids immediately C-terminal to the cysteine in a fixed pharmaceutical composition or it may be adminis palmitoylation site are not deleted. tered separately, before, simultaneously with or after the 0081. In one embodiment, a region containing the binding other drug Substance. Such anti-inflammatory drugs include region of antibody 5 described below (i.e., a region containing steroids, in particular glucocorticosteroids Such as budes nine amino acids at the amino-terminal end of the B2ARIC3 onide, beclamethasone, fluticasone, ciclesonide or mometa loop (I233-V242), having the amino acid sequence IDKSEG sone or steroids described in WO 0200679 especially those of RFHV: SEQID NO:3 and also containing L266 and/or K270 Examples 3, 11, 14, 17, 19, 26, 34, 37, 39, 51, 60, 67, 72,73, from the C-terminal end of the B2AR IC3 loop) may be 90, 99 and 101, LTB4 antagonists such as those described in substituted into a different (non-(B2AR) GPCR at the same U.S. Pat. No. 5,451,700, LTD4 antagonists such as mon US 2011/0166330 A1 Jul. 7, 2011

telukast and Zafirlukast, and PDE4 inhibitors such as ArifloR) standing that they are being offered to illustrate the present (GlaxoSmith Kline), Roflumilast (Byk Gulden), V-11294A invention and should not be construed in any way as limiting (Napp), BAY19-8004 (Bayer), SCH-351591 (Schering its scope. Plough), Arofylline (Almirall Prodesfarma), PD189659 (Parke-Davis), AWD-12-281 (Asta Medica), CDC-801 (Cel Example 1 gene) and KW-4490 (Kyowa Hakko Kogyo) and A2a agonists Antigen Production such as those described in EP 1052264, EP 1241176, WO 0091 Antigen was prepared by reconstituting purified, 0023457, WO0077018, WO 0123399, WO 0160835, WO functional BAR at high density into phospholipid vesicles (1 0194368, WO 0200676, WO 0222630, WO 0296462, WO mg receptor per mg of phospholipids) using the following 0127130, WO 0127131, WO 9602543, WO 9602553, WO method. 98.28319, WO9924449, WO 9924.450, WO 9924.451, WO 0092 BAR having an amino terminal Flag epitope tag 9938877, WO994.1267, WO 9967263, WO 9967264, WO and a carboxylhexahistidine tag was expressed in Sf9 insects 9967265, WO 9967266, WO 94.17090, EP 409595A2 and cells and purified by sequential M1 antibody and alprenolol WO 0078774 and A2b antagonists such as those described in affinity chromatography as previously described (Kobilka WO 02/42298. Such bronchodilatory drugs include anticho Anal Biochem 1995 231,269-71). Purified BAR was immo linergic or antimuscarinic agents, in particular ipratropium bilized on a Ni column and equilibrated with 10 column bromide, oxitropium bromide and tiotropium bromide. In volumes of a mixture of 5 mg/ml DOPC (Avanti Polar Lipids) general terms, these protocols involve administering to an and 0.5 mg/ml Lipid A (Sigma) in 1% (w/v) octylglucoside individual suffering from a GPCR-related disorder an effec (Anatrace), 100 mM. NaCl, 20 mM Hepes pH 7.5 and 1 uM tive amount of an antibody that modulates a GPCR to modu carazolol (a BAR antagonist). The BAR was then eluted in late the GPCR in the host and treat the individual for the the same buffer containing 200 mM imidazole. The concen disorder. tration of the eluted BAR was adjusted to 5 mg/ml. This I0086. In some embodiments, where a reduction in activity usually involved diluting the protein with the same buffer, but of a certain GPCR is desired, one or more compounds that occasionally required concentrating the protein up to two decrease the activity of the GPCR may be administered, fold with an Amicon ultrafiltration cell (100 kDa pore). The whereas when an increase in activity of a certain GPCR is protein was then dialyzed against phosphate buffered saline desired, one or more compounds that increase the activity of containing 1 uM carazolol at 4°C. to remove detergent. The the GPCR activity may be administered. reconstituted protein was stored at -80° C. prior to use for 0087. A variety of individuals are treatable according to immunization. the Subject methods. Generally such individuals are mam 0093. The phospholipid environment ensures the func mals or mammalian, where these terms are used broadly to tional integrity of the protein after injection into mice. To describe organisms which are within the class mammalia, provide additional stability, the AR was liganded with cara including the orders carnivore (e.g., dogs and cats), rodentia Zolol, a high affinity inverse agonist. To facilitate the immune (e.g., mice, guinea pigs, and rats), and primates (e.g., humans, response, phospholipid vesicles consisted of a 10:1 mixture chimpanzees, and monkeys). In many embodiments, the indi (by weight) of DOPC and the adjuvant Lipid A. The generated viduals will be humans. Subject treatment methods are typi vesicles contained randomly oriented fAR, so that both cally performed on individuals with such disorders or on cytoplasmic and extracellular domains are presented to individuals with a desire to avoid contracting such disorders. immune cells. 0088 A variety of publications describe treatment regi mens using the antibodies including, for example, published Example 2 patent applications 20080159981, 2008.0102069, Antibody Production 20070142346, 20060018899, 2005O1486O7 and 20030228663, as well as U.S. Pat. Nos. 7,306,801, 6,399,063, 0094 Monoclonal antibodies (MABs) were generated 6,387.371 and 6,165,464, which are each incorporated by using a conventional fusion protocol, as follows: reference in their entirety. In general terms, these documents described methods including administering a therapeutic Myeloma Cell Lines monoclonal antibody to a Subject, singly or in combination (0095. The P3x63Ag8.653 myeloma cell line (ATCC # with another agent. The subject may then be monitored for a CRL-1580; Lot No. 1131010) was used for the fusion experi clinically beneficial response, where a beneficial response to ment performed with splenocytes from immunized mice. the antibody can be assessed according to whether an indi vidual patient experiences a desirable change in disease sta Cell Culture tuS 0096. Myeloma cells were propagated in Dulbecco's 0089. In particular embodiments, the antibody may have a Modified Eagle's Medium (DMEM-high glucose) supple translocation sequence (e.g., an HIV TAT. AntP, or VP22 mented with 10% Fetal Bovine Serum (FBS), 0.15g/L oxalo traslocation sequence, or other short sequence rich in basic acetate, 0.05 g/L pyruvate, 0.0082 g/L bovine insulin (OPI amino acids) which facilitates translocation of the antibody supplement), 10% NCTC 109 medium and 4 mM across the plasma membrane into the cytoplasm of a target L-glutamine. This formulation is referred to the SDMEM cell. Such translocation sequences and their use are known formulation. Newly formed hybridoma were selected in and reviewed in, for example, Gupta (Drug Deliv. Rev. 2005 SDMEM supplemented with HAT mixture (1.0x10 M 57:637-51), Steffen (Methods Mol. Biol. 2001 161:141-8) Hypoxanthine, 40x10 MAminopterin, 1.6x10M thymi and Hansen (Scientific World Journal. 2005 5:782-8). dine), 5% hybridoma cloning factor, gentamicin (50 ug/ml) 0090. In order to further illustrate the present invention, and 3-mercaptoethanol at 0.055 mM. This formulation is the following specific examples are given with the under referred as SDMEM-HAT. After selection, the newly formed US 2011/0166330 A1 Jul. 7, 2011

hybridomas were propagated in SDMEM supplemented with native receptor in fixed cells (see FIG. 4). The reduced bind 2% hybridoma cloning factor HT mixture (1.0x10 M ing of antibody 5 and antibody 9 to SDS denatured BAR hypoxanthine, 1.6x10 M thymidine). This formulation is showed that these antibodies bind to a three-dimensional referred as DMEM-HT. For in vitro antibody production, the epitope. hybridomas were propagated in SDMEM supplemented with 0.100 Antibodies 2, 5, 6, 7 and 9 all reacted with intracel 1% hybridoma cloning factor and 5-10% low-IgG FBS. lular epitopes. To select for antibodies that may interact with IC3, we examined the effect of antibody binding on the fluo Cell Fusion Protocol rescence of BAR labeled at C265 (at the cytoplasmic end of TM6) with tetramethylrhodamine. Tetramethylrhodamine 0097 Balb/c mice were immunized weekly with 30 ug of bound to C265 is predicted to lie at the interface between TM5 BAR in liposomes. The mice were injected intraperitoneally and TM6. Previous studies have shown that tetramethyl with 15ug of antigen and Subcutaneously at 2 sites with 7.5 rhodamine binding to C265 is sensitive to ligand-induced mg of antigen. Final boosts of 10 ug of BAR were given three dimensional changes in the BAR (Swaminath et al., J. intraperitoneally and intravenously on day 3 and 4 before Biol. Chem. 2004 279: 686-691). As such, antibodies binding fusion. Spleens were harvested aseptically, placed in cold to IC3 may stabilize a specific conformation of TM5 relative DMEM, diced and homogenized. The homogenate was cen to TM6 that would be detected by a change in tetramethyl trifuged at 1000 rpm for 5 minutes. The cell pellet was incu rhodamine fluorescence. It can be seen that antibody 5 bated with 5 ml of Redcell lysis buffer (Sigma R7757) for 3-5 induced the largest fluorescence response and had the highest mins. DMEM (20 ml) was added and the cells were centri fuged at 1000 rpm for 5 minutes. The pellet was rinsed twice affinity for the BAR (FIG. 2B). The fluorescence change in 20 ml DMEM. The final pellet was resuspended in 30 mL induced by antibody 5 was significantly greater than the DMEM. Spleen and myeloma cells were combined at a 3:1 response to antibody 9, the other intracellular binder that ratio, centrifuged (1000 rpm) and resuspend in DMEM. The reacted weakly to SDS denatured receptor. It is notable that centrifugation was repeated and 1 mL PEG-1500 (50% solu there was a response to antibody 8 and antibody 4, two anti tion) was added to the cell pellet over 3 min with gentle bodies that bind to an extracellular epitope. This suggests that mixing. 4 mL of SDMEM was slowly added to cells over 2 binding of these antibodies to the extracellular surface of the min. After 1 min incubation, 20 mL of SDMEM was added fAR influences the structure around the cytoplasmic end of over 1 min. The suspension was centrifuge (1000 rpm) and TM6. the pellet was resuspended in a total of 30 mL HAT-SDMEM 0101 Based on the results of assays shown in FIGS. 2A and incubate at 37° C. for 2 hours. HAT-SDMEM media was and 2B antibody 5 was chosen for crystallography experi ments. Antibody 5 bound to an intracellular epitope, it exhib added to achieve a cell density of 5x10" cells/well and dis ited relatively high affinity for native BAR (FIG. 2B), but pensed into 96-well plates at 200 uL per well. Cells were bound weakly to SDS denatured protein (FIG. 2A). Antibody incubated for 11 days before screening media for antibody 5 also induced the largest fluorescence response in BAR production. labeled at C265 with tetramethylrhodamine. Based on these 0098 Fusions from two mice yielded seventeen hybri experiments, antibody 5 binds to a three dimensional epitope doma clones that produced antibody against faR as deter on the native third intracellular loop. mined by an ELISA assay on immobilized phospholipid vesicles containing purified BAR. Nine of these hybridomas produced sufficient quantities offAR-specific antibody for Example 4 further characterization. The antibodies were characterized Antibody Characterization as binding the intracellular or extracellular surface of the receptor in immunofluorescence experiments with HEK-293 0102 Fab 5 fragments were generated from purified anti cells stably expressing an N-terminally FLAG-tagged version body 5 by papain cleavage and purified by ion exchange of the BAR. Antibodies that recognize an intracellular chromatography. The dissociation constant for Fab 5 binding epitope only stain permeabilized cells. Staining of cells that to purified BAR was determined to be 150 nM by isothermal were either fixed or fixed and permeabilized indicated that titration calorimetry (FIG. 5). As expected, this value is five of the antibodies bound to the intracellular face and four higher than the EC50 (23 nM) observed for the intact anti bound to the extracellular surface (FIG. 4). body in the fluorescence experiments (FIG. 2B). 0103) To localize the intracellular epitope of the AR that Example 3 interacts with Fab 5, limited tryptic digestions of purified BAR were performed. Cleavage of purified BAR with Antibody Screening trypsin yielded two bands with molecular weights of approxi mately 27 and 29 kDa on a Western blot probed with the M1 0099 Antibodies were screened for binding to a three anti-FLAG antibody (FIG.3A). The sizes of these fragments dimensional epitope on the three-dimensional Surface on the indicate trypsin digestion at two often potential sites in IC3 IC3 of the native f3AR, rather than a flexible linear epitope. (FIG. 3A). When preincubated with Fab 5, the 27 kDa band Nine MABs were screened, along with positive (M1 anti disappears Suggesting that the antibody binds to one of the body) and negative (9E10) controls, for binding to BAR amino-terminal trypsin sites in IC3 (FIG. 3A). denatured with sodium dodecyl sulfate (SDS) and spotted on 0104. The effect of Fab binding on ligand binding proper nitrocellulose (FIG. 2A). Antibody 5 and antibody 9 showed ties and on agonist-induced three dimensional changes was the weakest binding to denatured protein, even though they determined. Fab 5 had no significant effect on antagonist or showed immunostaining comparable to M1 on binding to agonist binding affinity (Table 1 below). US 2011/0166330 A1 Jul. 7, 2011

has since produced diffraction quality crystals and a 3.4 A TABLE 1. structure of the Fab 5-fAR complex. Antagonist and agonist binding properties of Example 5 the BAR with and without prebound Fab 5. Preparation of Fab Fragments Hidihydroalprenolol Isoproterenol 0109 Monoclonal mouse immunoglobulins against the K. : S.E. K. S.E. interval B2AR reconstituted in liposomes were raised, as described (nM) (nM) above. Mab5 IgGs from mouse hybridoma cell culture super natant were purified using a Protein G column (Pierce). Fab5 B2AR 1.02 O.O9 290 (269-311 fragments were generated by papain proteolysis (Worthing B2AR-Fab5 1.08 O.OS 329 (310-348) ton) and purified by Mono Q chromatography. The fragments Saturation and competition binding assays were performed on purified B2AR reconstituted were concentrated to ~100 mg ml with a Millipore concen in phospholipid vesicles in the absence and presence of prebound Fab 5. Values are from three independent experiments performed intriplicate. The IC50 values used for calculations trator (5 kDa molecular weight cut off) in a solution of 10 mM of K values were obtained from means of pC50 values determined by nonlinear regression analysis and the S.E. interval from plC50+ S.E. HEPES pH 7.5 and 100 mM NaCl. Example 6 0105 IC3 is known to be important for G protein activa Preparation of B2AR365-Fab5 Complexes tion. Fab 5 prevented coupling of purified BAR to purified G 0110. The BAR365 was expressed in Sf-9 insect cells protein (data not shown), most likely due to steric competi infected with BAR365 baculovirus, and solubilized accord tion. However, it is possible that Fab 5 restricts the confor ing to previously described methods. Functional protein was mational changes associated with receptor activation. The obtained by M1 FLAG affinity chromatography (Sigma) effect of Fab binding on agonist-induced conformational prior to and following alprenolol-Sepharose chromatogra changes was determined using a fluorescence-based assay phy. Receptor bound alprenolol was exchanged for carazolol (Yao et al. Nat. Chem. Biol. 2006 2, 417-422). on the second M1 resin. N-linked glycolsylations were 0106 Purified receptor was reacted with 1:1 equivalent of removed by treatment with PNGaseF (NEB), and the FLAG monobromobimane (mBBr, Invitrogen) in buffer A (100 mM epitope was removed by treatment with AcTEV protease NaCl, 20 mM HEPES, pH 7.5, 0.1% dodecyl maltoside) and (Invitrogen). Protein was concentrated to ~50 mg/ml with a incubated overnight on ice in the dark. The fluorophore 100 kDa molecular weight cut off Vivaspin concentrator labeled receptor was purified right before use by gel filtration (Vivascience) and mixed in stoichiometric excess of Fab5. on a desalting column equilibrated with buffer B. Fluores The complex was purified on a Superdex-200 (10/300GL) cence spectroscopy experiments were performed on a Spex column in a solution of 10 mM HEPES pH 7.5, 100 mM FluoroMax-3 spectrofluorometer (Jobin Yvon Inc, NJ) with NaCl, 0.1% dodecylmaltoside, and 10 uM carazolol. The photon counting mode by using an excitation and emission purified AR365-Fab5 complexes were concentrated to ~60 bandpass of 4 nm. All experiments were performed at 25°C. mg ml using a Vivaspin concentrator. For emission scans, excitation was set at 370 nm and emission Example 7 was measured from 430-530 nm with an integration time of 1 Crystallization s/nm. To determine the effect of Fab5 antibody and drug, 0111. The BAR365-Fab5 complexes were mixed with three individual labeled protein samples were incubated with bicelles (10% w/v 3:1 DMPC:CHAPSO in 10 mM HEPES antibody (1 uM Fab5) or 100LLM Isoproterenol or both. Emis pH 7.5, 100 mM. NaCl) at a 1:5 (protein: bicelle) ratio, and sion spectra of the samples were taken after 15 minutes incu crystals were grown in sitting- and hanging-drop formats at bation. Fluorescence intensity was corrected for background 22°C. using equal Volumes of protein mixture and reservoir fluorescence from buffer and ligands in all experiments. The Solutions. Initial crystallization leads were identified using data are the meantS.E. of two independent experiments per multiple 96-well sitting-drop screens from Nextal (Qiagen). formed in triplicate. After extensive optimization, crystals for data collection were 0107 Agonist binding induces a change that brings the grown in hanging-drop format over a reservoir Solution of to fluorophore monobromobimane bound to C271 at the cyto 1.85-2.0 M ammonium sulfate, 180 mM sodium acetate, 5 plasmic end of TM6 closer to W 135 at the cytoplasmic end of mM EDTA, 100 mM MES or HEPES pH 6.5-7.5. Crystals TM3 resulting in a decrease in bimane fluorescence. This grew to full size within 7 to 10 days. Crystals were flash fluorescence change was not affected by binding of antibody frozen and stored in liquid nitrogen, with reservoir Solution 5 (FIG. 3B). In conclusion, while Fab 5 required a native plus 20% glycerol as cryoprotectant. f3AR to bind, it did not restrict the movement of transmem brane segments involved in ligand binding and agonist acti Example 8 Vation. Microcrystallography Data Collection and Process 0108. To more easily identify crystals of the Fab 5-BAR ing complex, we labeled purified AR at C265 with tetrameth 0112 Microbeams were employed for data collection. The ylrhodamine (BAR-TMR). The Fab 5-3AR-TMR complex shape of the crystals permitted complete data to be measured was formed by mixing BAR-TMR with a stoichiometric from a single crystal. A Small wedge of data, typically 5-10'. excess of Fab 5 and isolating the complex by size exclusion (1 perframe) could be measured before significant radiation chromatography. Small fluorescent crystals formed by vapor damage was observed. The crystal was then translated to a phase diffusion using ammonium sulfate as the precipitant new, undamaged position to collect the next wedge of data. A (FIG. 6). Importantly, no crystals formed from BAR alone or total of 182° of data collected in this manner, measured at from Fab 5 alone under these conditions, showing that the beamline ID23-2 of the ESRF, were used for the final additional protein interactions and the stabilizing effects of |BAR365-Fab5 data set (Table 2). The BAR24/365-Fab5 the antibody were critical for successful crystallization of the data set was obtained from 225° of data measured on beam BAR. Further refinement of the crystallography conditions line 23ID-B of the APS (Table 2). US 2011/0166330 A1 Jul. 7, 2011 11

TABLE 2 X-ray data collection and refinement statistics BAR365-Fab5 BAR24/365-Fab5 Data collection Space group Cell dimensions a, b, c (A) 338.4, 48.5, 89.4 338.4, 48.5, 89.4 Cl, f, Y () 90., 104.6, 90. 90., 104.6, 90. Resolution (A) 86.4-3.4 (3.49-3.40) * 50-3.4 (3.52-3.40) * R nerge 0.117 (0.407) 0.120 (0.456) foI 9.9 (2.3) 7.8 (2.6) Completeness (%) 98.9 (94.9) 99.4 (98.4) Multiplicity 3.3 (2.9) 4.1 (3.4) Refinement Resolution (A) 20.-3.4 20.-3.4 No. reflections work? free 17658,1902 17458,1886 RworkRfee 0.216.0.269 O.226.O.279 No. atoms 4.905 4887 Average B values (A)

Receptor 156. 187. Fab5 67. 91. Overallanisotropic B (A) B11/B2/B33/B13 -27.1, 31.3 -4.24.4 -16.8. 20.4-3.5.12.4 R.m. S deviations

Bond lengths (A) O.OO7 O.OO8 Bond angles () 1.4 1.5 Ramachandran plot ** receptor? Fab5

% most favored 76.3/71.5 75.8, 71.8 allowed 22.1.27.2 22.1.26.6 generously allowed 1.61.3 2.1.1.6 disallowed 0.00.0 0.00.0 * Highest resolution shell is shown in parenthesis. ** As defined in PROCHECK

0113 ESRF data were processed with MOSFLM and Using a partial specific volume of 1.21 A/Da for protein, the SCALA (Collaborative Computational Project, N. Acta Cryst unit cell would have 66% lipid, detergent and aqueous solvent 1994 D50, 760-763) and data measured at the APS were for is one BAR-Fab5 complex in the asymmetric unit. The processed with HKL2000 (Otwinowski et al. Methods Enzy structure of the BAR365-Fab5 complex was solved by mol. 1997 276, 307-326). In many cases it was necessary to molecular replacement, by searching with separate constant reindex the crystal after moving to a new position on the and variable domain models against a low resolution (4.1 A) crystal, which may have been due to bending of the frozen data set measured at ESRF beamline ID-13. crystals such that the indexing matrix from the previous Vol 0114. The crystal structure confirms that Fab 5 binds to a ume could not accurately predict the diffraction pattern from three dimensional epitope consisting of nine amino acids at a new volume. This problem precluded global postrefinement the amino-terminal end of IC3 (I233-V242). The antibody of the unit cell parameters. The unit cell parameters used for also binds two amino acids at the carboxyl-terminal end subsequent analysis (Table 1) were obtained from initial (L266 and K270), but at a different region of the antibody. indexing and refinement from one wedge of the ESRF data, FIG. 7 illustrating packing of B2AR-Fab complex in a crystal, and were Subsequently found to be sufficient for processing and FIG. 8 schematically illustrates the three-dimensional the remaining data without unit cell constant refinement. epitope to which the Fab 5 antibody binds.

SEQUENCE LISTING

<16 Os NUMBER OF SEO ID NOS: 3

<21 Os SEQ ID NO 1 &211s LENGTH: 214 212s. TYPE: PRT US 2011/0166330 A1 Jul. 7, 2011 12

- Continued

<213> ORGANISM; mus musculis 22 Os. FEATURE: <221s NAME/KEY: UNSURE <222s. LOCATION: (0) . . . (O) <223> OTHER INFORMATION: Fab5 light chain <4 OOs, SEQUENCE: 1 Asp Ile Llys Met Thr Glin Ser Pro Ser Ser Met Tyr Ala Ser Leu Gly 1. 5 1O 15 Glu Arg Val Thir Ile Thr Cys Lys Ala Ser Glin Asp Ile Asin Ser Tyr 2O 25 3O Lieu. Ser Trp Phe Glin Gln Lys Pro Gly Lys Ser Pro Llys Thr Lieu. Ile 35 4 O 45 Tyr Arg Ala Asn Arg Lieu Val Asp Gly Val Pro Ser Arg Phe Ile Gly SO 55 6 O Thr Gly Ser Gly Glin Asp Tyr Ser Lieu. Thir Ile Ser Ser Lieu. Asp Tyr 65 70 7s 8O Glu Asp Met Gly Ile Tyr Tyr Cys Lieu. Glin Tyr Asp Glu Phe Pro Tyr 85 90 95 Thir Phe Gly Gly Gly Thr Llys Lieu. Glu Ile Lys Arg Ala Asp Ala Ala 1OO 105 11 O Pro Thr Val Ser Ile Phe Pro Pro Ser Ser Glu Gln Lieu. Thir Ser Gly 115 12 O 125 Gly Ala Ser Val Val Cys Phe Lieu. ASn ASn Phe Tyr Pro Lys Asp Ile 13 O 135 14 O Asn. Wall Lys Trp Llys Ile Asp Gly Ser Glu Arg Glin Asn Gly Val Lieu 145 150 155 160 Asn Ser Trp Thr Asp Glin Asp Ser Lys Asp Ser Thr Tyr Ser Met Ser 1.65 17O 17s Ser Thr Lieu. Thir Lieu. Thir Lys Asp Glu Tyr Glu Arg His Asn Ser Tyr 18O 185 19 O Thr Cys Glu Ala Thr His Lys Thr Ser Thr Ser Pro Ile Val Lys Ser 195 2OO 2O5 Phe Asn Arg Asn. Glu. Cys 21 O

<210s, SEQ ID NO 2 &211s LENGTH: 217 212. TYPE: PRT <213> ORGANISM; mus musculis 22 Os. FEATURE: <221s NAME/KEY: UNSURE <222s. LOCATION: (0) . . . (O) <223> OTHER INFORMATION: Fab 5 Heavy chain <4 OOs, SEQUENCE: 2 Glu Val Glin Lieu. Glin Glin Ser Gly Ala Glu Lieu Ala Arg Pro Gly Ala 1. 5 1O 15 Ser Val Lys Lieu Ser Cys Lys Ala Ser Gly Tyr Ile Phe Thr Asp Tyr 2O 25 3O Tyr Ile Asn Trp Val Arg Glin Arg Thr Gly Glin Gly Phe Glu Trp Ile 35 4 O 45 Gly Glu Ile Tyr Pro Gly Ser Gly Asn Ile Asp Tyr Asn Glu Arg Phe SO 55 6 O Lys Asp Lys Ala Thr Lieu. Thir Ala Asp Llys Ser Ser Ser Thir Ala Tyr 65 70 7s 8O US 2011/0166330 A1 Jul. 7, 2011 13

- Continued

Met Glin Luell Ser Ser Lieu. Thir Ser Glu Asp Ser Ala Wall Tyr Phe Cys 85 90 95

Wall Arg Gly Phe Gly Tyr Trp Gly Glin Gly. Thir Thr Lieu. Thir Wall Ser 1OO 105 11 O

Ser Ala Lys Th Thir Pro Pro Ser Wall Tyr Pro Leu. Ala Pro Gly Ser 115 12 O 125

Ala Ala Gn. Thir Asn. Ser Met Val Thir Lieu. Gly Cys Lieu. Wall Gly 13 O 135 14 O

Tyr Phe Pro Glu Pro Wall Thir Wall. Thir Trp ASn Ser Gly Ser Luell Ser 145 150 155 160

Ser Gly Wall His Thir Phe Pro Ala Wall Lieu. Glin Ser Asp Luell Tyr Thr 1.65 17O 17s

Leul Ser Ser Ser Wall. Thir Wall Pro Ser Ser Thr Trp Pro Ser Glu Thir 18O 185 19 O

Wall. Thir Cys Asn Wall Ala His Pro Ala Ser Ser Thr Lys Wall Asp Llys 195 2O5

Ile Val Pro Arg Asp Cys Gly 21 O 215

<210s, SEQ ID NO 3 &211s LENGTH: 10 212. TYPE: PRT <213> ORGANISM: homo sapien <4 OOs, SEQUENCE: 3 Ile Asp Llys Ser Glu Gly Arg Phe His Val 1. 5 1O

1. A monoclonal antibody that specifically binds a three a) reconstituting a GPCR in artificial phospholipid vesicles dimensional epitope on the intracellular region (IC3) loop of to make an antigen; and a GPCR, wherein said monoclonal antibody is characterized b) immunizing an animal with said antigen. in that it: 22. The monoclonal antibody of claim 1, wherein said a) stabilizes the relative conformations of the transmem monoclonal antibody is rabbit, mouse or chicken. 23. The monoclonal antibody of claim 1, wherein said brane region 5 (TM5) and transmembrane region 6 GPCR is a receptor for a biogenic amine. (TM6) of said GPCR, 24. The monoclonal antibody of claim 1, wherein said b) facilitates crystallization of said GPCR. GPCR is a dopamine receptor. 2. The monoclonal antibody of claim 1, wherein said anti 25. The monoclonal antibody of claim 1, wherein said body specifically binds the IC3 loop of the B2 adrenoreceptor. GPCR is not a 32-. 3. The monoclonal antibody of claim 1, wherein said anti 26. The monoclonal antibody of claim 1, wherein said body is a monovalent antibody. GPCR is a seratonin receptor. 4-17. (canceled) 27. The monoclonal antibody of claim 1, wherein said 18. The monoclonal antibody of claim 1, wherein said GPCR is an adrenergic receptor. monoclonal antibody is a single chain antibody. 28. The monoclonal antibody of claim 1, wherein said GPCR is a subtype 4. 19. The monoclonal antibody of claim 1, wherein said 29. The monoclonal antibody of claim 1, wherein said monoclonal antibody is a Fab fragment. GPCR is a ghrelin receptor. 20. The monoclonal antibody of claim 1, wherein said 30. The monoclonal antibody of claim 1, wherein said monoclonal antibody comprises a light chain variable domain GPCR is a metabotropic . of SEQID NO. 1 and a heavy chain variable domain of SEQ 31. The monoclonal antibody of claim 1, wherein said ID NO:2. GPCR is a chemokine receptor. 21. The monoclonal antibody of claim 1, wherein said monoclonal antibody is made by c c c c c