METHOD FOR ANALYZING THE THREE DIMENSIONAL STRUCTURE OF A GPCR

Certain embodiments provide a method for crystallizing a GPCR. The method may employ a fusion protein comprising, from N-terminus to C-terminus: a) a first portion of a family C G-protein coupled receptor (GPCR), wherein the first portion comprises the TM1, TM2 and TM3, regions of the GPCR; b) a stable, folded protein insertion; and c) a second portion of the GPCR, wherein the second portion comprises the TM4, TM5 TM6 and TM7 regions of the GPCR.

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Description

CROSS-REFERENCING

This application claims the benefit of U.S. provisional patent application Ser. No. 61/378,332, filed on Aug. 30, 2010, which application is incorporated herein in its entirety.

GOVERNMENT RIGHTS

This work was supported in part by Small Business Innovation Research grant number R43MH088091-01. The federal government has certain rights in this invention.

BACKGROUND

G-protein-coupled receptors (GPCRs) are a large family of proteins that are involved in a wide range of functions (including various autocrine, paracrine and endocrine processes). GPCRs show considerable diversity at the sequence level and can be separated into distinct families on the basis of their sequence.

The family C GPCR receptors (which are also known as family 3 GPCRs) are generally composed of four elements: an N-terminal signal sequence, a large hydrophilic extracellular agonist-binding region containing several conserved cysteine residues which may be involved in disulphide bonds, a shorter region containing seven transmembrane domains, and a C-terminal cytoplasmic domain of variable length (see, e.g., Bräuner-Osborne, Curr. Drug Targets 2007 8: 169-84). Family C GPCR members include the metabotropic glutamate receptors, the extracellular calcium-sensing receptors, the gamma-amino-butyric acid (GABA) type B receptors, and the vomeronasal type-2 receptors, for example (see, e.g., Tanabe Neuron 1992 8: 169-79; Brown, Nature 1993 366: 575-80; Sullivan, J. Pharmacol. Exp. Ther. 2000 293: 460-7; and Ryba, Neuron 1997 19: 371-9).

As family C GPCRs are involved in many important physiological processes, they are promising targets for drug development.

SUMMARY OF THE INVENTION

A fusion protein is provided. In certain embodiments, the fusion protein comprises: a) a first portion of a family C G-protein coupled receptor (GPCR), where the first portion comprises the TM1, TM2 and TM3 regions of the GPCR; b) a stable, folded protein insertion, e.g., the amino acid sequence of lysozyme; and c) a second portion of the GPCR, where the second portion comprises the TM4, TMS, TM6 and TM7 regions of the GPCR. The polypeptide may be employed in crystallization methods, for example.

In certain embodiments, the stable, folded protein insertion is a polypeptide than can fold autonomously in a variety of cellular expression hosts, and is resistant to chemical and thermal denaturation. In particular embodiments, the stable folded protein insertion may be a protein that is known to be highly crystallizable, in a variety of space groups and crystal packing arrangements. In certain cases, the stable, folded protein insertion may also shield the fusion protein from proteolysis between the TM3 and TM4 domains, and may itself be protease resistant. Lysozyme is one such polypeptide, however many others are known.

Also provided is a nucleic acid encoding the above described fusion protein, and a cell comprising the same. The fusion protein may be disposed on the plasma membrane of the cell.

Also provided are crystals comprising the above described fusion protein, folded into an active form.

The above-described cell may be employed in a method comprising: culturing the cell to produce the fusion protein; and isolating the fusion protein from the cell. The method may further comprise crystallizing the fusion protein to make crystals which, in certain embodiments, may involve combining the fusion protein with lipid prior to crystallization. In certain embodiments, the fusion protein is crystallized using a bicelle crystallization method or a lipidic cubic phase crystallization method. The method may further comprise obtaining atomic coordinates of the fusion protein from the crystal.

Also provided is a method of determining a crystal structure. This method may comprise receiving an above described fusion protein, crystallizing the fusion protein to produce a crystal; and obtaining atomic coordinates of the fusion protein from the crystals. In other embodiments, the method may comprise forwarding a fusion protein to a remote location where the protein may be crystallized and analyzed, and receiving the atomic coordinates of the fusion protein.

In particular embodiments, a composition comprising a fusion protein in crystalline form is provided in which the fusion protein comprises, from N-terminus to C-terminus: a) a first portion of a family C G-protein coupled receptor (GPCR), wherein the first portion comprises TM1, TM2, and TM3 regions of the GPCR; b) a domain comprising the amino acid sequence of a lysozyme; and c) a second portion of the GPCR, wherein the second portion comprises TM4, TMS, TM6 and TM7 regions of the GPCR.

In particular embodiments, the first and second portions of the GPCR comprise the amino acid sequence of a naturally occurring GPCR.

In other embodiments, the first and second portions of the GPCR comprise the amino acid sequence of a non-naturally occurring GPCR.

In some embodiments, the first portion or the second portion of the GPCR comprises an affinity tag.

The domain, in certain cases, may comprise an amino acid sequence having at least 80% identity to the amino acid sequence of a wild-type lysozyme. For example, in certain cases, the domain may comprise an amino acid sequence that is at least 95% identical to the amino acid sequence of T4 lysozyme.

In particular embodiments, the GPCR may selected from the group consisting of: calcium-sensing receptor (CASR), GPRC6A (GPRC6A), GABAB receptor 1 (GABBR1); GABAB receptor 2 (GABBR2), GPR156 (GPR156), mGluR1 (GRM1), mGluR2 (GRM2), mGluR3 (GRM3), mGluR4 (GRM4), mGluR5 (GRM5), mGluR6 (GRM6), mGluR7 (GRM7) mGluR8 (GRM8), RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), RAIG4 (GPRC5D), taste receptor, type 1, member 1 (TAS1R1), taste receptor, type 1, member 2 (TAS1R2), taste receptor, type 1, member 3 (TAS1R3), GPR158 (GPR158), GPR179 (GPR179); bride of sevenless protein and vomeronasal receptor, type 2.

In some embodiments, the fusion protein is bound to a ligand for the GPCR.

In particular embodiments, the domain of b) spaces the C-terminal end of the TM3 region and the N-terminal end of the TM4 region of the GPCR such that the closest alpha carbon atoms at the C-terminal end and the N-terminal end are spaced by a distance in the range of from 6 Å to 16 Å.

Also provided is a composition comprising a polypeptide in crystalline form, wherein the polypeptide comprises, from N-terminus to C-terminus: a) a first portion of a family C G-protein coupled receptor (GPCR), wherein the first portion comprises the amino acid sequence that is N-terminal to the IC2 loop of the GPCR; b) a domain comprising the amino acid sequence of a lysozyme; and c) a second portion of the GPCR, wherein the second portion comprises the amino acid sequence that is C-terminal to the IC2 loop of the GPCR.

Also provided is a composition comprising a polypeptide in crystalline form, wherein the polypeptide comprises: a G-protein coupled receptor (GPCR) comprising an IC2 loop comprising the amino acid sequence of a lysozyme.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 is a schematic illustration of a GPCR, showing the canonical transmembrane regions (TM1, TM2, TM3, TM4, TM5, TM6, and TM7), intracellular regions (IC1, IC2, and IC3), and extracellular regions (EC1, EC2, and EC3).

FIG. 2 is a schematic illustration of a subject fusion protein, showing a stable, folded protein insertion between the TM3 and TM4 regions of a GPCR.

FIG. 3 shows the amino acid and nucleotide sequences of an exemplary lysozyme fusion protein.

FIGS. 4A-4G show exemplary the amino acid sequences of several representative family C GPCRs, and an insertion point for a stable, folded protein insertion in each of the GPCRs. The TM3 and TM4 regions of each of the GPCRs is bolded and underlined in these figures.

FIG. 5 shows the amino acid sequences of exemplary stable, folder protein insertions that may be employed in a subject fusion protein.

FIG. 6 shows two graphs and a table demonstrating that MPEP has same affinity for mGluR5 as Rock10, the fusion protein defined in FIG. 3.

DEFINITIONS

Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, New York (1994), and Hale & Marham, THE HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, NY (1991) provide one of skill with general dictionaries of many of the terms used in this disclosure. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described.

All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference.

Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.

The headings provided herein are not limitations of the various aspects or embodiments of the invention which can be had by reference to the specification as a whole. Accordingly, the terms defined immediately below are more fully defined by reference to the specification as a whole.

“G-protein coupled receptors” or “GPCRs” are polypeptides that share a common structural motif, referred to herein as the “heptahelical domain”, having seven regions of between 22 to 24 hydrophobic amino acids that form seven alpha helices, each of which spans a membrane. As illustrated in FIG. 1, each span is identified by number, i.e., transmembrane-1 (TM1), transmembrane-2 (TM2), etc. The transmembrane helices are joined by regions of amino acids between transmembrane-2 and transmembrane-3, transmembrane-4 and transmembrane-5, and transmembrane-6 and transmembrane-7 on the exterior, or “extracellular” side, of the cell membrane, referred to as “extracellular” regions 1, 2 and 3 (EC1, EC2 and EC3), respectively. The transmembrane helices are also joined by regions of amino acids between transmembrane-1 and transmembrane-2, transmembrane-3 and transmembrane-4, and transmembrane-5 and transmembrane-6 on the interior, or “intracellular” side, of the cell membrane, referred to as “intracellular” regions 1, 2 and 3 (IC1, IC2 and IC3), respectively. The “carboxy” (“C”) terminus of the receptor lies in the intracellular space within the cell, and the “amino” (“N”) terminus of the receptor lies in the extracellular space outside of the cell. GPCR structure and classification is generally well known in the art, and further discussion of GPCRs may be found in Probst, DNA Cell Biol. 1992 11:1-20; Marchese et al Genomics 23: 609-618, 1994; and the following books: Jurgen Wess (Ed) Structure-Function Analysis of G Protein-Coupled Receptors published by Wiley-Liss (1st edition; Oct. 15, 1999); Kevin R. Lynch (Ed) Identification and Expression of G Protein-Coupled Receptors published by John Wiley & Sons (March 1998) and Tatsuya Haga (Ed), G Protein-Coupled Receptors, published by CRC Press (Sep. 24, 1999); and Steve Watson (Ed) G-Protein Linked Receptor Factsbook, published by Academic Press (1st edition; 1994). A schematic representation of a typical GPCR is shown in FIG. 1.

A “family C” GPCR shares its plasma membrane topology with other GPCRs, as it is composed of an extracellular amino terminal domain (ATD) that is commonly referred to as having a bi-lobular “Venus-flytrap” module (VFTM), seven transmembrane spanning segments separated by alternating intracellular and extracellular loops (the “heptahelical domain”), and an intracellular carboxy terminal region. The most notable structural feature of the family C receptors is an unusually large ADT (up to 500-600 in length in certain cases) that contains the binding site for the endogenous agonist of the receptor. Unless otherwise indicated, if a particular GPCR is referred to herein (e.g., “mGluR5”) the reference is to the receptor from humans as well as the ortholog of that receptor from other species (e.g., other mammals such as mouse, non-human primates, rat, dog, etc).

The term “naturally-occurring” in reference to a GPCR means a GPCR that is naturally produced (for example and not limitation, by a mammal or by a human). Such GPCRs are found in nature. The term “non-naturally occurring” in reference to a GPCR means a GPCR that is not naturally-occurring. Wild-type GPCRs that have been made constitutively active through mutation, and variants of naturally-occurring GPCRs, e.g., epitope-tagged GPCR and GPCRs lacking their native N-terminus are examples of non-naturally occurring GPCRs. Non-naturally occurring versions of a naturally occurring GPCR are activated by the same ligand as the naturally-occurring GPCR.

The term “ligand” means a molecule that specifically binds to a GPCR. A ligand may be, for example a polypeptide, a lipid, a small molecule, an antibody. A “native ligand” is a ligand that is an endogenous, natural ligand for a native GPCR. A ligand may be a GPCR “antagonist”, “agonist”, “partial agonist” or “inverse agonist”, or the like.

A “modulator” is a ligand that increases or decreases a GPCR intracellular response when it is in contact with, e.g., binds, to a GPCR that is expressed in a cell. This term includes agonists, including partial agonists and inverse agonists, and antagonists.

A “deletion” is defined as a change in either amino acid or nucleotide sequence in which one or more amino acid or nucleotide residues, respectively, are absent as compared to an amino acid sequence or nucleotide sequence of a parental GPCR polypeptide or nucleic acid. In the context of a GPCR or a fragment thereof, a deletion can involve deletion of about 2, about 5, about 10, up to about 20, up to about 30 or up to about 50 or more amino acids. A GPCR or a fragment thereof may contain more than one deletion.

An “insertion” or “addition” is that change in an amino acid or nucleotide sequence which has resulted in the addition of one or more amino acid or nucleotide residues, respectively, as compared to an amino acid sequence or nucleotide sequence of a parental GPCR. “Insertion” generally refers to addition to one or more amino acid residues within an amino acid sequence of a polypeptide, while “addition” can be an insertion or refer to amino acid residues added at an N- or C-terminus, or both termini. In the context of a GPCR or fragment thereof, an insertion or addition is usually of about 1, about 3, about 5, about 10, up to about 20, up to about 30 or up to about 50 or more amino acids. A GPCR or fragment thereof may contain more than one insertion. Reference to particular GPCR or group of GPCRs by name, e.g., reference to the serotonin or histamine receptor, is intended to refer to the wild type receptor as well as active variants of that receptor that can bind to the same ligand as the wild type receptor and/or transduce a signal in the same way as the wild type receptor.

A “substitution” results from the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively as compared to an amino acid sequence or nucleotide sequence of a parental GPCR or a fragment thereof. It is understood that a GPCR or a fragment thereof may have conservative amino acid substitutions which have substantially no effect on GPCR activity. By conservative substitutions is intended combinations such as gly, ala; val, ile, leu; asp, glu; asn, gln; ser, thr; lys, arg; and phe, tyr.

The term “biologically active”, with respect to a GPCR, refers to a GPCR having a biochemical function (e.g., a binding function, a signal transduction function, or an ability to change conformation as a result of ligand binding) of a naturally occurring GPCR.

As used herein, the terms “determining,” “measuring,” “assessing,” and “assaying” are used interchangeably and include both quantitative and qualitative determinations. Reference to an “amount” of a GPCR in these contexts is not intended to require quantitative assessment, and may be either qualitative or quantitative, unless specifically indicated otherwise.

The terms “polypeptide” and “protein”, used interchangeably herein, refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.

The term “fusion protein” or grammatical equivalents thereof is meant a protein composed of a plurality of polypeptide components, that while typically unjoined in their native state, are joined by their respective amino and carboxyl termini through a peptide linkage to form a single continuous polypeptide. Fusion proteins may be a combination of two, three or even four or more different proteins. The term polypeptide includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; fusion proteins with detectable fusion partners, e.g., fusion proteins including as a fusion partner a fluorescent protein, β-galactosidase, luciferase, etc.; and the like.

The terms “nucleic acid molecule” and “polynucleotide” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. Non-limiting examples of polynucleotides include a gene, a gene fragment, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, control regions, isolated RNA of any sequence, nucleic acid probes, and primers. The nucleic acid molecule may be linear or circular.

As used herein the term “isolated,” when used in the context of an isolated compound, refers to a compound of interest that is in an environment different from that in which the compound naturally occurs. “Isolated” is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified.

As used herein, the term “substantially pure” refers to a compound that is removed from its natural environment and is at least 60% free, at least 75% free, or at least 90% free from other components with which it is naturally associated.

A “coding sequence” or a sequence that “encodes” a selected polypeptide, is a nucleic acid molecule which can be transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide, for example, in a host cell when placed under the control of appropriate regulatory sequences (or “control elements”). The boundaries of the coding sequence are typically determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus. A coding sequence can include, but is not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic DNA sequences from viral or prokaryotic DNA, and synthetic DNA sequences. A transcription termination sequence may be located 3′ to the coding sequence. Other “control elements” may also be associated with a coding sequence. A DNA sequence encoding a polypeptide can be optimized for expression in a selected cell by using the codons preferred by the selected cell to represent the DNA copy of the desired polypeptide coding sequence.

“Operably linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. In the case of a promoter, a promoter that is operably linked to a coding sequence will effect the expression of a coding sequence. The promoter or other control elements need not be contiguous with the coding sequence, so long as they function to direct the expression thereof. For example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the coding sequence and the promoter sequence can still be considered “operably linked” to the coding sequence.

By “nucleic acid construct” it is meant a nucleic acid sequence that has been constructed to comprise one or more functional units not found together in nature. Examples include circular, linear, double-stranded, extrachromosomal DNA molecules (plasmids), cosmids (plasmids containing COS sequences from lambda phage), viral genomes comprising non-native nucleic acid sequences, and the like.

A “vector” is capable of transferring gene sequences to a host cell. Typically, “vector construct,” “expression vector,” and “gene transfer vector,” mean any nucleic acid construct capable of directing the expression of a gene of interest and which can transfer gene sequences to host cells, which can be accomplished by genomic integration of all or a portion of the vector, or transient or inheritable maintenance of the vector as an extrachromosomal element. Thus, the term includes cloning, and expression vehicles, as well as integrating vectors.

An “expression cassette” comprises any nucleic acid construct capable of directing the expression of a gene/coding sequence of interest, which is operably linked to a promoter of the expression cassette. Such cassettes can be constructed into a “vector,” “vector construct,” “expression vector,” or “gene transfer vector,” in order to transfer the expression cassette into a host cell. Thus, the term includes cloning and expression vehicles, as well as viral vectors.

A first polynucleotide is “derived from” or “corresponds to” a second polynucleotide if it has the same or substantially the same nucleotide sequence as a region of the second polynucleotide, its cDNA, complements thereof, or if it displays sequence identity as described above.

A first polypeptide is “derived from” or “corresponds to” a second polypeptide if it is (i) encoded by a first polynucleotide derived from a second polynucleotide, or (ii) displays sequence identity to the second polypeptides as described above.

The term “stable, folded protein insertion” refers to a folded region of polypeptide that is inserted between two neighboring domains (e.g., the TM3 and TM4 domains of a GPCR), such that the domains are spaced relative to each other at a distance that allows them to interact as in the wild-type protein. When folded, such a domain does not readily become inactive or denatured. The term “stable, folded protein insertion” excludes an amino acid sequence of a fluorescent protein (e.g., GFP, CFP or YFP), and excludes amino acid sequences that are at least 90% identical to the entire IC2 loop of another wild type GPCR. The IC2 loop of a wild type GPCR does not contain stable, folded protein domain.

The term “active form” or “native state” of a protein is a protein that is folded in a way so as to be active. A GPCR is in its active form if it can bind ligand, alter conformation in response to ligand binding, and/or transduce a signal which may or may not be induced by ligand binding. An active or native protein is not denatured.

The term “stable domain” is a polypeptide domain that, when folded in its active form, is stable, i.e., does not readily become inactive or denatured.

The term “folds autonomously” indicates a protein that folds into its active form in a cell, without biochemical denaturation and renaturation of the protein, and without chaperones.

The term “naturally-occurring” refers to an object that is found in nature.

The term “non-naturally-occurring” refers to an object that is not found in nature.

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

In the following description, the fusion protein is described first, followed by a discussion of the crystallization method in which the fusion protein may be employed.

Fusion Proteins

As noted above, a fusion protein is provided. In certain embodiments, the fusion protein comprises: a) a first portion of a family C G-protein coupled receptor (GPCR), where the first portion comprises the TM1, TM2 and TM3 regions of the GPCR; b) a stable, folded protein insertion c) a second portion of the GPCR, where the second portion comprises the TM4, TM5, TM6 and TM7 regions of the GPCR. In particular embodiments, the stable, folded protein insertion spaces the ends of the TM3 region and the TM4 region of the GPCR at a distance (e.g., in the range of 6 Å to 16 Å) that does not abolish the activity of the GPCR. The stable, folded protein insertion provides a polar surface area for crystal lattice contacts, allowing the protein to be crystalized.

In very general terms, such a protein may be made by inserting into the IC2 region of the GPCR a stable, folded protein that holds the two flanking portions of the GPCR (i.e. the portion that lies N-terminal to the IC2 region and the portion that lies C-terminal to the IC2 region) together at a distance that is compatible with a functional GPCR in terms of pharmacologic and dynamic properties. For clarity, the terms “inserting” includes inserting a sequence between two amino acids in an existing region as well as inserting a sequence into a region in which amino acids have been deleted. As such, an “insertion” may be made by inserting a sequence between two amino acid residues in an IC2 region, or by replacing (i.e., substituting) at least one amino acid residue in an IC2 region with a sequence.

GPCRs

Any family C GPCR is suitable for use in the subject methods, as long as it has TM3 and TM4 regions that are identifiable in the sequence of the GPCR. A discussion of the phylogenetic relationships between the different family C GPCRs are reviewed in Brauner-Osborne, (Curr Drug Targets 2007 8: 169-84), Wellendorph (Br J Pharmacol. 2009 156:869-84) and Hermans (Biochem J. 2001 359: 465-84), which are incorporated by reference for disclosure of a description of the structural and functional characteristics of family C GPCRs, as well examples of the same.

Family C GPCRs include: a) Calcium-sensing receptor-related GPCRs, including: calcium-sensing receptor (CASR) and GPRC6A (GPRC6A); b) GABAB (gamma-aminobutyric acid) receptors, including: GABAB receptor 1 (GABBR1); GABAB receptor 2 (GABBR2) and GPR156 (GPR156); c) metabotropic glutamate receptors (mGluR), including: mGluR1 (GRM1), mGluR2 (GRM2), mGluR3 (GRM3), mGluR4 (GRM4), mGluR5 (GRM5), mGluR6 (GRM6), mGluR7 (GRM7) and mGluR8 (GRM8); d) retinoic acid-inducible orphan G protein-coupled receptors (RAIG), including; RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C) and RAIG4 (GPRC5D); e) taste receptors, including: taste receptor, type 1, member 1 (TAS1R1), taste receptor, type 1, member 2 (TAS1R2), taste receptor, type 1, member 3 (TAS1R3); 0 orphan receptors, e.g., GPR158 (GPR158) and GPR179 (GPR179); and g) other GPCRs including the bride of sevenless protein vomeronasal receptor, type 2. Amino acid sequences of a representative number of Family C receptors are set forth in FIG. 4.

It is recognized that both native (naturally occurring) and altered native (non-naturally occurring) GPCRs may be used in the subject methods. In certain embodiments, therefore, an altered native GPCR (e.g. a native GPCR that is altered by an amino acid substitution, deletion and/or insertion) such that it binds the same ligand as a corresponding native GPCR, and/or couples to a G-protein as a result of the binding. In certain cases, at least the heptahelical domain of a GPCR employed herein may have an amino acid sequence that is at least 80% identical to, e.g., at least 90% identical, at least 85% identical, at least 90% identical, at least 95% identical, or at least 98% identical, to the corresponding sequence of a naturally occurring GPCR. A GPCR employed herein may optionally contain the extracellular amino terminal domain of a GPCR, and/or the C-terminal domain of a GPCR. Without the extracellular amino terminal domain, a Family C GPCR does not bind the native ligand. However, such a GPCR does bind allosteric modulators and can activate G proteins (see, e.g., Goudet et al. Proc. Natl. Acad. Sci. 2004 101: 378-383). Positive allosteric modulators (PAMs) enhance signalling whereas negative allosteric modulators (NAMs) dampen the response to ligand. In certain cases, however, a full length receptor may be employed. In other words, in certain embodiments, a native GPCR may be “trimmed back” from its N-terminus and/or its C-terminus to leave its heptahelical domain, prior to crystallization.

In the subject methods, the region between the TM3 and TM4 regions of a GPCR (i.e., the IC2 region) is usually identified, and the amino acid sequence of a stable, folded insertion protein is inserted into that region to form a fusion protein. The stable, folded protein insertion spaces the TM3 and TM4 regions relative to one another. A schematic representation of the prototypical structure of a GPCR is provided in FIG. 1, where these regions, in the context of the entire structure of a GPCR, may be seen. A schematic representation of a subject fusion protein is shown in FIG. 2. In one embodiment, the IC2 loop of the GPCR is contains a stable, folded protein insertion. In particular embodiment, amino acids may be deleted from the IC2 loop of the GPCR in addition to inserting the stable, folded protein insertion into the loop.

The IC2 region of a GPCR lies in between transmembrane regions TM3 and TM4 and, may be in the range of about 15 amino acids to about 30 amino acids in length, for example. The TM3, IC2, and TM4 regions are readily discernable by one of skill in the art using, for example, a program for identifying transmembrane regions; once transmembrane regions TM3 and TM4 regions are identified, the IC2 region will be apparent. The TM3, IC2, and TM5 regions may also be identified using such methods as pairwise or multiple sequence alignment (e.g. using the GAP or BESTFIT of the University of Wisconsin's GCG program, or CLUSTAL alignment programs, Higgins et al., Gene. 1988 73:237-44), using a target GPCR and, for example, GPCRs of known structure.

Suitable programs for identifying transmembrane regions include those described by Moller et al., (Bioinformatics, 17:646-653, 2001). A particularly suitable program is called “TMHMM” Krogh et al., (Journal of Molecular Biology, 305:567-580, 2001). To use these programs via a user interface, a sequence corresponding to a GPCR or a fragment thereof is entered into the user interface and the program run. Such programs are currently available over the world wide web, for example at the website of the Center for Biological Sequence Analysis at cbs.dtu.dk/services/. The output of these programs may be variable in terms its format, however they usually indicate transmembrane regions of a GPCR using amino acid coordinates of a GPCR.

When TM regions of a GPCR polypeptide are determined using TMHMM, the prototypical GPCR profile is usually obtained: an N-terminus that is extracellular, followed by a segment comprising seven TM regions, and further followed by a C-terminus that is intracellular. TM numbering for this prototypical GPCR profile begins with the most N-terminally disposed TM region (TM1) and concludes with the most C-terminally disposed TM region (TM7).

Accordingly, in certain embodiments, the amino acid coordinates of the TM3, IC-2, and TM4 regions of a GPCR are identified by a suitable method such as TMHMM.

In certain cases, once the TM3-IC2-TM4 segment is identified for a GPCR, a suitable region of amino acids is chosen for substitution with the amino acid sequence of the a stable, folded protein insertion. In certain embodiments, the substituted region may be identified using conserved or semi-conserved amino acids in the TM3 and TM4 transmembrane regions. In certain embodiments and depending on the GPCR used, the N-terminus of the stable, folded protein insertion is linked to the amino acid that is 15 to 25 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25; e.g., 20-23) residues C-terminal to a conserved tyrosine in the TM3 of the GPCR, although linkages outside of this region are envisioned. In certain embodiments and depending on the GPCR used, the C-terminus of the stable, folded protein insertion may be linked to the amino acid that is 10 to 20 (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20; e.g., 15-18) residues N-terminal a conserved glutamine in the beginning of the TM4 region of the GPCR, although linkages outside of this region are envisioned. In certain cases, the insertion may be placed between two amino acids in the IC2 region. Depending on which GPCR is being used, the insertion may placed immediately C-terminal to the amino acid that is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 24, or 26 amino acids C-terminal of the end of the TM3 region, for example. In particular embodiments, this position may be optimized.

For GPCRs that contain no conserved tyrosine residue in TM3 or glutamine residue in TM4, positions for inserting an a stable, folded protein insertion can be determined based on two considerations: a) alignment of the sequence of the GPCR with receptor members of the same subfamily (which contained conserved proline residues in TM3 or TM4; b) by identifying the juxtaposition to the TM3/TM4 regions by hydrophobicity analysis.

In addition to introducing a stable, folded protein insertion into the IC2 region of a GPCR, as described above, in certain cases, the C-terminal region of the GPCR (which in some GPCRs may be C-terminal to a cysteine palmitoylation site, may be deleted. In certain cases, the 20-30 amino acids immediately C-terminal to the cysteine palmitoylation site are not deleted.

Stable, Folded Protein Insertions

In certain embodiments, a stable, folded protein insertion of a subject fusion protein may be a soluble, stable protein (e.g., a protein displaying resistance to thermal and chemical denaturation) that folds autonomously of the GPCR portion of the fusion protein, in a cell. In certain cases, the stable, folded protein insertion may have no cysteine residues (or may be engineered to have no cysteine residues) in order to avoid potential disulphide bonds between the stable, folded protein insertion and a GPCR portion of the fusion protein, or internal disulphide bonds. Stable, folded protein insertions are conformationally restrained, and are resistant to protease cleavage.

In certain cases, stable, folded protein insertions may contain most or all of the amino acid sequence of a polypeptide that is readily crystallized. Such proteins may be characterized by a large number of deposits in the protein data bank (www.rcsb.org) in a variety of space groups and crystal packing arrangements. While examples that employ lysozyme as stable, folded protein insertion are discussed below, the general principles may be used to employ any of a number of polypeptides that have the characteristics discussed above. Suitable stable, folded protein insertion candidates include those containing the amino acid sequence of proteins that are readily crystallized including, but not limited to: lysozyme, glucose isomerase, xylanase, trypsin inhibitor, crambin, ribonuclease. Other suitable polypeptides may be found at the BMCD database (Gilliland et al 1994. The Biological Macromolecule Crystallization Database, Version 3.0: New Features, Data, and the NASA Archive for Protein Crystal Growth Data. Acta Crystallogr. D50 408-413), as published to the world wide web.

In certain embodiments, the stable, folded protein insertion used may be at least 80% identical (e.g., at least 85% identical, at least 90% identical, at least 95% identical or at least 98% identical to a wild type protein. Many suitable wild type proteins, including non-naturally occurring variants thereof, are readily crystalizable.

In one embodiment, the autonomously folding stable domain may be of the lysozyme superfamily, which share a common structure and are readily crystallized. Such proteins are described in, e.g., Wohlkönig et al (Structural Relationships in the Lysozyme Superfamily: Significant Evidence for Glycoside Hydrolase Signature Motifs. PLoS ONE 2010 5: e15388).

As noted above, one such stable, folded protein insertion that may be employed in a subject fusion protein is lysozyme. Lysozyme is a highly crystallizable protein (see, e.g., Strynadka et al Lysozyme: a model enzyme in protein crystallography EXS 1996 75: 185-222) and at present over 200 atomic coordinates for various lysozymes, including many wild-type lysozymes and variants thereof, including lysozymes from phage T4, human, swan, rainbow trout, guinea fowl, soft-shelled turtle, tapes japonica, nurse shark, mouse sperm, dog, chicken, hen, cow, and phage P1, as well as man-made variants thereof, have been deposited in NCBI's structure database. A subject fusion protein may contain any of a wide variety of lysozyme sequences. See, e.g., Strynadka et al (Lysozyme: a model enzyme in protein crystallography (EXS. 1996; 75:185-222), Evrard et al (Crystal structure of the lysozyme from bacteriophage lambda and its relationship with V and C-type lysozymes) J. Mol. Biol. 1998 276:151-64), Forsythe et al (Crystallization of chicken egg-white lysozyme from ammonium sulfate. Acta Crystallogr D Biol Crystallogr. 1997 53:795-7), Remington et al (Structure of the Lysozyme from Bacteriophage T4: An Electron Density Map at 2.4A Resolution), Lyne et al (Preliminary crystallographic examination of a novel fungal lysozyme from Chalaropsis. J Biol Chem. 1990 265:6928-30), Marana et al. (Crystallization, data collection and phasing of two digestive lysozymes from Musca domestica. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 62:750-2), Harada et al (Preliminary X-ray crystallographic study of lysozyme produced by Streptomyces globisporus. J Mol Biol. 1989 207:851-2) and Yao et al (Crystallization and preliminary X-ray structure analysis of pigeon egg-white lysozyme). J. Biochem. 1992 111:1-3).

The length of the stable, folded protein insertion may be between 80-500 amino acids, e.g., 100-200 amino acids in length, although stable, folded protein insertions having lengths outside of this range are also envisioned.

As noted above, the stable, folded protein insertion is not fluorescent or light-emitting. As such, the stable, folded protein insertion is not CFP, GFP, YFP, luciferase, or other light emitting, fluorescent variants thereof. In certain cases, a stable, folded protein insertion region does not contain a flexible polyglycine linker or other such conformationally unrestrained regions. In certain cases, the stable, folded protein insertion contains a sequence of amino acids from a protein that has a crystal structure that has been solved. In certain cases, the stable, folded protein insertion should not have highly flexible loop region characterized by high crystallographic temperature factors (i.e., high B-factors).

In certain cases, once a suitable polypeptide is identified, a stable, folded protein insertion may be designed by deleting amino acid residues from the N-terminus, the C-terminus or both termini of the polypeptide such that the closest alpha carbon atoms in the backbone at the termini of the polypeptide are spaced by a distance of in the range of 6 Å to 16 Å, e.g., 7 Å to 15 Å, 7 Å to 10 Å, 12 Å to 15 Å, 10 Å to 13 Å, or about 11 Å (i.e. 10 Å to 12 Å). The stable, folded protein insertion, disposed between the TM3 and TM4 regions of a GPCR, spaces those regions by that distance. The distance may be modified by adding or removing amino acids to or from the stable, folded protein insertion.

The amino acid sequence for an exemplary lysozyme fusion protein is set forth in FIG. 3. FIG. 4 shows exemplary insertion points for a representative selection of family C GPCRs. The amino acid sequences of exemplary alternative insertions (which may be substituted into any of the sequences of FIG. 4 in place of the lysozyme sequence) are shown in FIG. 5. These sequences include the sequences of trypsin inhibitor, calbindin, barnase, xylanase and glucokinase although other sequences can be readily used.

Nucleic Acids

A nucleic acid comprising a nucleotide sequence encoding a subject fusion protein is also provided. A subject nucleic acid may be produced by any method. Since the genetic code and recombinant techniques for manipulating nucleic acid are known, the design and production of nucleic acids encoding a subject fusion protein is well within the skill of an artisan. In certain embodiments, standard recombinant DNA technology (Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995; Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, (1989) Cold Spring Harbor, N.Y.) methods are used.

For example, site directed mutagenesis and subcloning may be used to introduce/delete/substitute nucleic acid residues in a polynucleotide encoding GPCR. In other embodiments, PCR may be used. Nucleic acids encoding a polypeptide of interest may also be made by chemical synthesis entirely from oligonucleotides (e.g., Cello et al., Science (2002) 297:1016-8).

In certain embodiments, the codons of the nucleic acids encoding polypeptides of interest are optimized for expression in cells of a particular species, particularly a mammalian, e.g., human, species. Vectors comprising a subject nucleic acid are also provided. A vector may contain a subject nucleic acid, operably linked to a promoter.

A host cell (e.g., a host bacterial, mammalian, insect, plant or yeast cell) comprising a subject nucleic acid is also provided as well a culture of subject cells. The culture of cells may contain growth medium, as well as a population of the cells. The cells may be employed to make the subject fusion protein in a method that includes culturing the cells to provide for production of the fusion protein. In many embodiments, the fusion protein is directed to the plasma membrane of the cell, and is folded into its active form by the cell.

The native form of a subject fusion protein may be isolated from a subject cell by conventional technology, e.g., by solubilization, precipitation, centrifugation, affinity, filtration or any other method known in the art. For example, affinity chromatography (Tilbeurgh et al., (1984) FEBS Lett. 16:215); ion-exchange chromatographic methods (Goyal et al., (1991) Biores. Technol. 36:37; Fliess et al., (1983) Eur. J. Appl. Microbiol. Biotechnol. 17:314; Bhikhabhai et al., (1984) J. Appl. Biochem. 6:336; and Ellouz et al., (1987) Chromatography 396:307), including ion-exchange using materials with high resolution power (Medve et al., (1998) J. Chromatography A 808:153; hydrophobic interaction chromatography (Tomaz and Queiroz, (1999) J. Chromatography A 865:123; two-phase partitioning (Brumbauer, et al., (1999) Bioseparation 7:287); ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; or size exclusion chromatography using, e.g., Sephadex G-75, may be employed.

In particular embodiments, the GPCR, e.g., the N- or C-terminus of the GPCR or an external loop of the GPCR, may be tagged with an affinity moiety, e.g., a his tag, GST, MBP, flag tag, or other antibody binding site, in order to facilitate purification of the GPCR fusion protein by affinity methods.

Before crystallization, a subject fusion protein may be assayed to determine if the fusion protein is active, e.g., can bind ligand and change in conformation upon ligand binding, and if the fusion protein is resistant to protease cleavage. Such assays are well known in the art.

In certain cases the subject fusion protein may be combined with a ligand for the GPCR of the fusion protein prior to crystallization.

Crystallization Methods

A subject fusion protein may be crystallized using any of a variety of crystallization methods, many of which are reviewed in Caffrey (Membrane protein crystallization. J Struct. Biol. 2003 142:108-32) and those that employ detergent micelles, bicelles and lipidic cubic phase (LCP). In general terms, the methods are lipid-based methods that include adding lipid to the fusion protein prior to crystallization. Such methods have previously been used to crystallize other membrane proteins. Many of these methods, including the lipidic cubic phase crystallization method and the bicelle crystallization method, exploit the spontaneous self-assembling properties of lipids and detergent as vesicles (vesicle-fusion method), discoidal micelles (bicelle method), and liquid crystals or mesophases (in meso or cubic-phase method). Lipidic cubic phases crystallization methods are described in, for example: Landau et al, Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc. Natl. Acad. Sci. 1996 93:14532-5; Gouaux, It's not just a phase: crystallization and X-ray structure determination of bacteriorhodopsin in lipidic cubic phases. Structure. 1998 6:5-10; Rummel et al, Lipidic Cubic Phases: New Matrices for the Three-Dimensional Crystallization of Membrane Proteins. J. Struct. Biol. 1998 121:82-91; and Nollert et al Lipidic cubic phases as matrices for membrane protein crystallization Methods. 2004 34:348-53, which publications are incorporated by reference for disclosure of those methods. Bicelle crystallization methods are described in, for example: Faham et al Crystallization of bacteriorhodopsin from bicelle formulations at room temperature. Protein Sci. 2005 14:836-40. 2005 and Faham et al, Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J Mol Biol. 2002 Feb. 8; 316(1):1-6, which publications are incorporated by reference for disclosure of those methods.

In particular cases, a GPCR may be crystallized using methods described in Rosenbaum et al (Nature. 2011 469:236-40), Cherezov et al (Science. 2007 318:1258-65), Rosenbaum (Science. 2007 318:1266-73) and Rasmussen et al (Nature. 2007 450:383-7), among others. Such methods have been used to crystallize other GPCRs containing a lysozyme fusion.

In particular embodiments, the GPCR may be co-crystallized with or tested for activity using an allosteric modulator for the GPCR. Exemplary allosteric modulators for Family C GPCRs include those listed in Table 1 and described in Table 2 of Conn (Nature Reviews: Drug Discovery 2009 8: 41-54; incorporated by references), which are shown below. Others are known.

TABLE 1 Receptor Modulator example(s) Calcium sensing Fendeline; cinacalcet; NPS 467; NPS 568; L- receptor amino acids; NPS 2143; calhex 231 GABA CGP7930; CGP13501; GS39783 mGluR1 (−)-C PC C OEt; Ro 67-7476; Ro 01-6128; BAY36-7620; [3H]R214127; NPS 2390; EM-TBPC; cis-64a; JNJ 16259685 mGluR2 LY487379; BINA; LY181837; Ro 67-6221 mGluR4 SIB-1893; MPEP; (−)-PHCCC; VU0155041; VU0080421 mGluR5 MPEP; MTEP; DFB; DCB; DMeOB; CPPHA; CDPPB: VU-29; ADX-47273 mGluR7 AMN082

TABLE 2 Potential indications for allosteric modulators of mGluRs compound name mglur compound structure (reference from Conn) subtype Pain CPCCOEt (27) 1 NAM Anxiety, fragile X syndrome, GERD, chronic pain, depression, migraine SIB-1757 (28) 5 NAM SIB-1893 (28) 5 NAM MPEP (29) 5 NAM MTEP (30) 5 NAM Fenobam (34) 5 NAM M-5MPEP (41) 5 Partial antagonist Br-5MPEPy (41) 5 Partial antagonist Schizophrenia, cognition, extinction DFB (48) 5 PAM CDPPB (51) 5 PAM ADX47273 (56) 5 PAM Anxiety disorders, schizophrenia LY354740 (58) 2/3 agonist LY341495 2/3 antagonist LY487379 (66) 2 PAM BINA (70) 2 PAM Parkinson's disease, movement disorders (−)-PHCCC (86.88) 4 PAM VU0155041 (87 4 PAM/ Allosteric agonist

Also provided is a method of determining a crystal structure. This method may comprise receiving an above described fusion protein, crystallizing the fusion protein to produce a crystal; and obtaining atomic coordinates of the fusion protein from the crystal. The fusion protein may be received from a remote location (e.g., a different laboratory in the same building or campus, or from a different campus or city), and, in certain embodiments, the method may also comprise transmitting the atomic coordinates, e.g., by mail, e-mail or using the internet, to the remote location or to a third party.

A method for producing a GPCR crystal is provided. This method may comprise: a) isolating a subject GPCR fusion protein; and b) crystallizing the isolated protein, thereby producing a GPCR crystal.

In other embodiments, the method may comprise forwarding a fusion protein to a remote location where the protein may be crystallized and analyzed, and receiving the atomic coordinates of the fusion protein.

Computer Modeling and Computer Systems

In certain embodiments, the above-described computer readable medium may further comprise programming for displaying a molecular model of a GPCR crystalized by the instant method, programming for identifying a compound that binds to the GPCR and/or a database of structures of known test compounds, for example. A computer system comprising the computer-readable medium is also provided. The model may be displayed to a user via a display, e.g., a computer monitor, for example.

The atomic coordinates may be employed in conjunction with a modeling program to provide a model of the GPCR. As used herein, the term “model” refers to a representation in a tangible medium of the three dimensional structure of the a GPCR or a complex of the same. For example, a model can be a representation of the three dimensional structure in an electronic file, on a display, e.g., a computer screen, on a piece of paper (i.e., on a two dimensional medium), and/or as a ball-and-stick figure. Physical three-dimensional models are tangible and include, but are not limited to, stick models and space-filling models. The phrase “imaging the model on a computer screen” refers to the ability to express (or represent) and manipulate the model on a computer screen using appropriate computer hardware and software technology known to those skilled in the art. Such technology is available from a variety of sources including, for example, Evans and Sutherland, Salt Lake City, Utah, and Biosym Technologies, San Diego, Calif. The phrase “providing a picture of the model” refers to the ability to generate a “hard copy” of the model. Hard copies include both motion and still pictures. Computer screen images and pictures of the model can be visualized in a number of formats including space-filling representations, backbone traces, ribbon diagrams, and electron density maps. Exemplary modeling programs include, but are not limited to PYMOL, GRASP, or O software, for example.

In another embodiment, the invention provides a computer system having a memory comprising the above-described atomic coordinates; and a processor in communication with the memory, wherein the processor generates a molecular model having a three dimensional structure representative of a a GPCR or a complex of the same. The processor can be adapted for identifying a candidate compound having a structure that is capable of binding to the a GPCR or a complex of the same, for example.

In the present disclosure, the processor may execute a modeling program which accesses data representative of the GPCR structure. In addition, the processor also can execute another program, a compound modeling program, which uses the three-dimensional model of the GPCR or a complex of the same to identify compounds having a chemical structure that binds to the GPCR or a complex of the same. In one embodiment the compound identification program and the structure modeling program are the same program. In another embodiment, the compound identification program and the structure modeling program are different programs, which programs may be stored on the same or different storage medium.

A number of exemplary public and commercial sources of libraries of compound structures are available, for example the Cambridge Structural Database (CSD), the Chemical Directory (ACD) from the company MDL (US), ZINC (Irwin and Shoichet, J. Chem. Inf Model. (2005) 45:177-82) as well as various electronic catalogues of publicly available compounds such as the National Cancer Institute (NCI, US) catalogue, ComGenex catalogue (Budapest, Hungary), and Asinex (Moscow, Russia). Such libraries may be used to allow computer-based docking of many compounds in order to identify those with potential to interact with the GPCR using the atomic coordinates described herein.

In certain cases, the method may further comprise a testing a compound to determine if it binds and/or modulates the GPCR or a complex of the same, using the atomic coordinates provided herein. In some embodiments, the method may further comprise obtaining the compound (e.g., purchasing or synthesizing the compound) and testing the compound to determine if it modulates (e.g., activates or inhibits) the GPCR e.g., acts an agonist, antagonist or inverse agonist of the GPCR).

In some embodiments, the method employs a docking program that computationally tests known compounds for binding to the GPCR or complex of the same. Structural databases of known compounds are known in the art. In certain cases, compounds that are known to bind and modulate the GPCR or complex of the same may be computationally tested for binding to GPCR or complex of the same, e.g., in order to identify a binding site and/or facilitate the identification of active variants of an existing compound. Such compounds include compounds that are know to be agonists of the GPCR. In other cases, the method may include designing a compound that binds to the GPCR, either de novo, or by modifying an existing compound that is known to bind to the GPCR.

A method that comprises receiving a set of atomic coordinates for the GPCR or complex of the same; and identifying a compound that binds to said GPCR or complex of the same using the coordinates is also provided, as is a method comprising: forwarding to a remote location a set of atomic coordinates for the GPCR or complex of the same; and receiving the identity of a compound that binds to the GPCR or complex of the same.

In certain embodiments, a computer system comprising a memory comprising the atomic coordinates of a GPCR or complex of the same is provided. The atomic coordinates are useful as models for rationally identifying compounds that bind to the GPCR or complex of the same. Such compounds may be designed either de novo, or by modification of a known compound, for example. In other cases, binding compounds may be identified by testing known compounds to determine if the “dock” with a molecular model of the GPCR. Such docking methods are generally well known in the art.

The structure data provided can be used in conjunction with computer-modeling techniques to develop models of ligand-binding sites on the GPCR or complex of the same selected by analysis of the crystal structure data. The site models characterize the three-dimensional topography of site surface, as well as factors including van der Waals contacts, electrostatic interactions, and hydrogen-bonding opportunities. Computer simulation techniques are then used to map interaction positions for functional groups including but not limited to protons, hydroxyl groups, amine groups, divalent cations, aromatic and aliphatic functional groups, amide groups, alcohol groups, etc. that are designed to interact with the model site. These groups may be designed into a candidate compound with the expectation that the candidate compound will specifically bind to the site.

The ability of a candidate compound to bind to a GPCR can be analyzed prior to actual synthesis using computer modeling techniques. Only those candidates that are indicated by computer modeling to bind the target with sufficient binding energy (i.e., binding energy corresponding to a dissociation constant with the target on the order of 10−2 M or tighter) may be synthesized and tested for their ability to bind to and modulate the GPCR. Such assays are known to those of skill in the art. The computational evaluation step thus avoids the unnecessary synthesis of compounds that are unlikely to bind the GPCR with adequate affinity.

A candidate compound may be computationally identified by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to associate with individual binding target sites on the GPCR. One skilled in the art may use one of several methods to screen chemical entities or fragments for their ability to associate with the GPCR, and more particularly with target sites on the GPCR. The process may begin by visual inspection of, for example a target site on a computer screen, based on the coordinates, or a subset of those coordinates. Selected fragments or chemical entities may then be positioned in a variety of orientations or “docked” within a target site of the GPCR as defined from analysis of the crystal structure data. Docking may be accomplished using software such as Quanta (Molecular Simulations, Inc., San Diego, Calif.) and Sybyl (Tripos, Inc. St. Louis, Mo.) followed by energy minimization and molecular dynamics with standard molecular mechanics forcefields such as CHARMM (Molecular Simulations, Inc., San Diego, Calif.) and AMBER (University of California at San Francisco).

Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include but are not limited to: GRID (Goodford, P. J., “A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules,” J. Med. Chem., 28, pp. 849-857 (1985)); GRID is available from Oxford University, Oxford, UK; MCSS (Miranker, A. and M. Karplus, “Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method,” Proteins: Structure, Function and Genetics, 11, pp. 29-34 (1991)); MCSS is available from Molecular Simulations, Inc., San Diego, Calif.; AUTODOCK (Goodsell, D. S. and A. J. Olsen, “Automated Docking of Substrates to Proteins by Simulated Annealing,” Proteins: Structure, Function, and Genetics, 8, pp. 195-202 (1990)); AUTODOCK is available from Scripps Research Institute, La Jolla, Calif.; DOCK (Kunts, I. D., et al. “A Geometric Approach to Macromolecule-Ligand Interactions,” J. Mol. Biol., 161, pp. 269-288 (1982)); DOCK is available from University of California, San Francisco, Calif.; CERIUS II (available from Molecular Simulations, Inc., San Diego, Calif.); and Flexx (Raret, et al. J. Mol. Biol. 261, pp. 470-489 (1996)).

Utility

The above-described crystals may be used to obtain to obtain the atomic coordinates of at least the heptahelical part of the fusion protein. In certain embodiments, a method for obtaining an X-ray diffraction pattern is provided. This method may generally comprise: a) exposing a crystal of a GPCR fusion protein to a source of X-rays, wherein the GPCR fusion protein is described above; and b) collecting an X-ray diffraction pattern for the crystal. In certain cases, the method may further comprises resolving the diffraction pattern to provide a set of atomic coordinates for the GPCR. The GPCR may be analyzed by a) obtaining atomic coordinates of a GPCR, wherein said atomic coordinates are produced by subjecting crystals of a subject GPCR fusion protein to X-ray diffraction analysis; and b) analyzing said GPCR using the atomic coordinates. In these embodiments, the obtaining can be receiving or accessing a file stored on a computer. The atomic coordinates may be provided on a computer readable medium. In certain embodiments, a computer readable storage medium comprising atomic coordinates for a GPCR is provided, where the atomic coordinates are produced by: a) producing crystals of a subject GPCR fusion protein; and b) subjecting the crystals to X-ray diffraction analysis. The crystals can be employed to design or identify compounds that modulate the GPCR.

In order to further illustrate certain aspects of the present invention, the following specific examples are given with the understanding that they are being offered to illustrate the present invention and should not be construed in any way as limiting its scope.

EXAMPLES

In order to obtain high-resolution structural information on the MGluR5, the T4 lysozyme (T4L) protein is inserted into the IC2 loop of the GPCR. The N- and C-terminal tails are also eliminated. The fusion protein is crystallized in lipidic cubic phase.

mGluR5 crystallization is done by inserting into the ICL2 of that protein a well-structured, soluble domain that aids in the formation of lattice contacts. The initial criteria for choosing the inserted soluble protein are that the amino and carboxyl termini would approximate the predicted distance between the cytoplasmic ends of helix III and helix IV, and that the protein would crystallize under a variety of conditions. T4L is a small, stable protein that fulfills these criteria.

DNA encoding the T4L protein (C54T, C97A) (M. Matsumura, W. J. Becktel, M. Levitt, B. W. Matthews, Proc. Natl. Acad. Sci. USA 86, 6562 (1989)) is initially cloned into the human mGluR5, between residues K677 and K678 (see FIG. 3). In addition, the receptor was truncated at both ends. Further optimization is carried out to reduce the length of the junction between the receptor and the T4L termini, to optimize expression and activity.

Methods

Molecular Biology for Generation of Mammalian and Sf9 Expression Constructs.

The insect cell expression plasmid that is used in this method is described in X. Yao et al., (Nat Chem Biol 2, 417 (2006). The wild-type coding sequence of the human mGluR5 (starting at Ser555) was cloned into the pFastbac1 Sf-9 expression vector (Invitrogen) with the Flag epitope tag at the amino terminus, and the construct was further modified. A synthetic DNA cassette encoding the T4 Lysozyme protein was made by overlapping extension PCR using 50-base oligonucleotides. This cassette was amplified and inserted into the mGluR5 construct between K677 and K678 (see FIG. 3), using the Quickchange Multi protocol (Stratagene). The corresponding mammalian cell expression plasmid is made by amplifying the entire fusion gene and cloning it into pCDNA3 (Invitrogen). Further deletions in the Sf9 and mammalian cell constructs are made using appropriate synthetic oligonucleotides in the Quickchange Multi protocol (Stratagene). The construct was confirmed by sequencing. The amino acid sequence of the encoded fusion protein is shown in FIG. 3.

Expression in HEK293 Cells and Functional Characterization by Ligand Binding.

HEK293 cells were cultured on plastic dishes at 37° C. with 5% CO2 in Dulbecco's modified Eagle's medium (Cellgro) with 5% fetal bovine serum. For an individual expression experiment, cells at confluency were split, and approximately 100,000 cells were used to seed glass cover slips in the same medium. After 2 d, cells are transfected with the addition of 1 μg of a given pCDNA3-receptor plasmid and 3 μl of Fugene 6 reagent (Roche). 48 h after transfection, cells were harvested and membranes prepared for ligand binding analysis. 3H-MPEP (a negative allosteric modulator that binds to the transmembrane domains of mGluR5) was used to detect functional mGluR5 in HEK293 cell membranes (see FIG. 6).

Expression and Purification of mGluR5-T4L from Baculovirus-Infected Sf9 Cells.

Recombinant baculovirus are made from pFastbac1-mGluR2-T4L using the Bac-to-Bac system (Invitrogen), as described previously (X. Yao et al., Nat Chem Biol 2, 417 (2006)). The mGluR5-T4L protein is expressed in Sf9 insect cells infected with this baculovirus, and solubilized according to previously described methods (B. K. Kobilka, Anal Biochem 231, 269 (1995)). Dodecylmaltoside-solubilized receptor with the N-terminal FLAG epitope (DYKDDDA) is purified by M1 antibody affinity chromatography (Sigma) and further purified by Sepharose chromatography to isolate only functional GPCR. Eluted receptor is re-bound to M1 FLAG resin, and ligand exchange is performed on the column. Protein is eluted from this final column with 0.2 mg/ml FLAG peptide in HLS buffer (0.1% dodecylmaltoside, 20 mM Hepes, 100 mM NaCl, pH 7.5) plus other reagents. Any N-linked glycolsylations is removed by treatment with PNGaseF (NEB). Protein is concentrated from ˜5 mg/ml to 50 mg/ml with a 100 kDa molecular weight cut-off Vivaspin concentrator (Vivascience), and dialyzed against HLS buffer plus other reagents.

Lipidic Cubic Phase Crystallization

For lipidic cubic phase (LCP) crystallization trials, trials are performed using an in meso crystallization robot. 24-well glass sandwich plates (S1, S2) are filled with 25 or 50 nL protein-laden LCP drops overlaid by 0.8 μL of precipitant solution in each well and sealed with a glass coverslip. All operations starting from mixing lipid and protein are performed at room temperature (˜21-23° C.). Trials are performed by varying the concentrations of, e.g., PEG 400, sodium sulfate, Bis-tris propane pH 6.5-7.0 and 1,4-butanediol using cholesterol in monoolein as the host lipid. Crystals are obtained in, e.g., 30-35% (v/v) PEG 400, 0.1-0.2 M sodium sulfate, 0.1 M Bis-tris propane pH 6.5-7.0 and 5-7% (v/v) 1,4-butanediol using 8-10% (w/w) cholesterol in monoolein as the host lipid. Other conditions may yield better crystals. PEG 400 and sulfate ion are used for crystallization, and the addition of cholesterol and 1,4-butanediol improved crystals size and shape enabling high-resolution diffraction. Additions of phospholipids (dioleoylphosphatidylcholine, dioleoylphosphatidylethanolamine, asolectin) alone and in combinations with cholesterol to the main host LCP lipid monoolein are also tried.

Crystal Harvesting

Crystals are harvested directly from the glass sandwich plates, even though these plates have been specifically designed for screening and optimization (S1, S2). Crystals are scooped directly from the LCP using 30 or 50 μm aperture MiTeGen MicroMounts and plunged into liquid nitrogen. Care is taken to drag as little as possible lipid around the crystal to decrease unwanted background scattering.

Data Collection

X-ray data is collected on the 23ID-B beamline (GM/CA CAT) at the Advanced Photon Source, Argonne, Ill. using a 10 μm minibeam (wavelength 1.0332 Å) and a MarMosaic 300 CCD detector. Several complete datasets are collected from single crystals at resolution expected to be between 2.8 and 3.5 Å using 5× attenuated beam, 5 s exposure and 1° oscillation per frame. Therefore, 10-20° wedges of high-resolution data could be collected from more than 40 crystals. Some of the best datasets are combined from independent crystals, scaling them against the lower resolution full dataset to obtain complete high resolution data.

Data Processing

Initial indexing of lattice parameters in spacegroup C2 and crystal orientation are performed using HKL2000. The refined lattice parameters and space group are implemented in the data processing program XDS for spot integration which models error explicitly for radiation decay, absorption, and rotation. The data, when obtained, is used as a scaling reference for incorporation of additional wedges of data collected at a much higher exposure. Each new dataset is indexed in XDS using the original unit cell parameters as constants which were then refined along with the crystal orientation, beam geometry, and mosaicity parameters. The refinement is generally stable, resulting in very similar unit cell constants which enabled subsequent scaling. All of the integrated wedges of data are then tested individually against the scaling reference set and included in the final scaled dataset if the merging statistics remained acceptable upon incorporation of the data. Each of the higher resolution datasets is exposed to a much larger dose of radiation resulting in a rapid decay in intensity. 10°-20° wedges are collected from each crystal or translation, 5°-7° of which expected to have a diffraction data to 2.4 Å. Based on the mean F/σ(F) of reflections near the three crystallographic axes, the effective resolution can be calculated. The anisotropy results in the high merging R factors in the last few resolution shells despite the significant I/σ(I) values. The anisotropy is either an inherent property of the crystals or the result of a preferential orientation of the crystals within the mounting loop. Thus, the higher resolution shells can be filled in anisotropically by incorporation of the additional data at high exposure levels, while the lower resolution shells have a very high redundancy and low anisotropy.

Claims

1-17. (canceled)

18. A method for analyzing the three dimensional structure of a GPCR on a computer system, comprising:

a) accessing a file containing atomic coordinates of a GPCR using a computer system that comprises a modeling program, wherein said atomic coordinates are produced by subjecting crystals of a GPCR fusion protein to X-ray diffraction analysis, wherein said GPCR fusion protein comprises, from N-terminus to C-terminus: i. a first portion of a G-protein coupled receptor (GPCR), wherein said first portion comprises the TM1, TM2 and TM3 regions of said GPCR; ii. a stable protein insertion that aids in the formation of lattice contacts; and iii. a second portion of said GPCR, wherein said second portion comprises the TM4, TM5 TM6 and TM7 regions of said GPCR;
b) modeling said atomic coordinates on said computer system using said modeling program to produce a model of the three dimensional structure of at least a portion of the GPCR; and
c) displaying the model of said three dimensional structure on the computer system.

19. The method of claim 18, wherein the GPCR fusion protein is co-crystallized with an allosteric modulator of GPCR.

20. The method of claim 18, wherein said stable, folded protein insertion element is a polypeptide that folds autonomously and is stable in its tertiary folded form.

21. The method of claim 18, wherein said stable, folded protein insertion comprises an amino acid sequence that is at least 95% identical to an amino acid sequence of a wild type protein.

22. The method of claim 18, wherein said stable, folded protein insertion comprises an amino acid sequence that is at least 95% identical to an amino acid sequence of T4 lysozyme.

23. The method of claim 18, further comprising identifying a potential modulator of said GPCR.

24. The method of claim 18, wherein said method comprises identifying a binding site for a modulator of said GPCR.

25. The method of claim 18, wherein said first and second portions of said GPCR comprise the amino acid sequence of a naturally occurring GPCR.

26. The method of claim 18, wherein said first and second portions of said GPCR comprise the amino acid sequence of a non-naturally occurring GPCR.

27. The method of claim 18, wherein the amino acid sequences of said first and second portions of said GPCR are least 80% identical to amino acid sequences of a naturally occurring GPCR.

28. The method of claim 18, wherein the GPCR of said fusion protein is a family C GPCR.

29. The method of claim 18, wherein said GPCR is a GABAB receptor.

30. The method of claim 18, wherein said GPCR is a metabotropic glutamate receptor.

31. The method of claim 18, wherein said GPCR comprises an amino acid sequence that is at least 95% identical to a calcium-sensing receptor (CASR), GPRC6A (GPRC6A), GABAB receptor 1 (GABBR1); GABAB receptor 2 (GABBR2), GPR156 (GPR156), mGluR1 (GRM1), mGluR2 (GRM2), mGluR3 (GRM3), mGluR4 (GRM4), mGluR5 (GRM5), mGluR6 (GRM6), mGluR7 (GRM7) mGluR8 (GRM8), RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), RAIG4 (GPRC5D), taste receptor, type 1, member 1 (TAS1R1), taste receptor, type 1, member 2 (TAS1R2), taste receptor, type 1, member 3 (TAS1R3), GPR158 (GPR158), GPR179 (GPR179); bride of sevenless protein and vomeronasal receptor, type 2.

32. A method for selecting a modulator of a GPCR, comprising:

a) accessing a file containing atomic coordinates of a GPCR using a computer system that comprises a modeling program, wherein said atomic coordinates are produced by subjecting crystals of a GPCR fusion protein to X-ray diffraction analysis, wherein said GPCR fusion protein comprises, from N-terminus to C-terminus: i. a first portion of a G-protein coupled receptor (GPCR), wherein said first portion comprises the TM1, TM2 and TM3 regions of said GPCR; ii. a stable protein insertion that aids in the formation of lattice contacts; and iii. a second portion of said GPCR, wherein said second portion comprises the TM4, TM5 TM6 and TM7 regions of said GPCR;
b) modeling said atomic coordinates on said computer system using said modeling program to produce a model of the three dimensional structure of at least the ligand binding site of the GPCR;
c) determining, using said computer system, whether a test compound docks with said binding site, wherein a test compound that docks with said binding site is a GPCR modulator; and
d) displaying on the computer system a model of said ligand binding site and said GPCR modulator, docked with said ligand binding site.

33. The method of claim 32, wherein the GPCR is co-crystallized with an allosteric modulator of GPCR.

34. The method of claim 32, wherein said stable, folded protein insertion comprises an amino acid sequence that is at least 95% identical to an amino acid sequence of a wild type protein.

35. The method of claim 32, wherein said first and second portions of said GPCR comprise the amino acid sequence of a naturally occurring GPCR.

36. The method of claim 32, wherein said first and second portions of said GPCR comprise the amino acid sequence of a non-naturally occurring GPCR.

37. The method of claim 32, wherein the amino acid sequences of said first and second portions of said GPCR are least 80% identical to amino acid sequences of a naturally occurring GPCR.

38. The method of claim 32, wherein the GPCR of said fusion protein is a family C GPCR.

39. The method of claim 32, wherein said GPCR comprises an amino acid sequence that is at least 95% identical to a calcium-sensing receptor (CASR), GPRC6A (GPRC6A), GABAB receptor 1 (GABBR1); GABAB receptor 2 (GABBR2), GPR156 (GPR156), mGluR1 (GRM1), mGluR2 (GRM2), mGluR3 (GRM3), mGluR4 (GRM4), mGluR5 (GRM5), mGluR6 (GRM6), mGluR7 (GRM7) mGluR8 (GRM8), RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), RAIG4 (GPRC5D), taste receptor, type 1, member 1 (TAS1R1), taste receptor, type 1, member 2 (TAS1R2), taste receptor, type 1, member 3 (TAS1R3), GPR158 (GPR158), GPR179 (GPR179); bride of sevenless protein and vomeronasal receptor, type 2.

40. A method for analyzing the three dimensional structure of a GPCR on a computer system, comprising:

a) accessing a file containing atomic coordinates of a GPCR using a computer system that comprises a modeling program, wherein said atomic coordinates are produced by subjecting crystals of a GPCR to X-ray diffraction analysis, wherein said GPCR comprises an IC2 loop containing a substitution that comprises the amino acid sequence of a stable protein insertion that aids in the formation of lattice contacts; and
b) modeling said atomic coordinates on said computer system using said modeling program to produce a model of the three dimensional structure of at least a portion of the GPCR; and
c) displaying the model of said three dimensional structure on the computer.

41. The method of claim 40, wherein said crystals comprise a ligand for said GPCR, and the method further comprises identifying the binding site for said ligand in said GPCR using said model.

42. The method of claim 41, wherein the analyzing comprises identifying amino acids that form polar contacts with said ligand in said binding site, using said model.

43. The method of claim 42, further comprising determining whether a test compound docks with said binding site using said model.

44. The method of claim 43, further comprising analyzing the packing of the test compound and amino acids in said binding site, using said model.

45. The method of claim 40, wherein said method further comprises making said test compound.

Patent History

Publication number: 20150057166
Type: Application
Filed: Oct 17, 2014
Publication Date: Feb 26, 2015
Inventor: BRIAN KOBILKA (Palo Alto, CA)
Application Number: 14/517,668