# Patent

## Title
Stabilized low affinity conformation of integrins for drug discovery

## Abstract

The methods and compositions described herein are based, in part, on the discovery that the introduction of a disulfide bond into an integrin polypeptide by the substitution of at least one cysteine residue in the polypeptide permits stabilization of the integrin in a “closed/inactive” state. This stabilizing disulfide bond permits integrins to be screened for a candidate molecule that can bind to the closed state. In particular, this approach can be used to screen for agents that bind to the closed state of an integrin polypeptide, and are useful as therapeutic treatments to prevent integrin activation.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/141,145 filed on Dec. 29, 2008, the contents of which are incorporated herein by reference in its entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted via EFS-Web as an ASCII copy and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 12, 2010, is named 03339306.txt, and is 170,131 bytes in size.
FIELD OF THE INVENTION
The field of the invention relates to stabilized integrins and uses thereof.
BACKGROUND
Integrins are cell adhesion receptors that transmit bidirectional signals across the plasma membrane and link the extracellular environment of a cell to the actin cytoskeleton. The conformation of the integrin extracellular domain and its affinity for ligand are dynamically regulated by a process termed “inside-out signaling.” Rapid upregulation of adhesiveness of integrins on platelets and white blood cells mediates hemostasis and leukocyte trafficking to sites of inflammation. By coupling to the actin cytoskeleton, integrins promote firm adhesion and provide traction for lamellipodium protrusion and locomotion. In migrating cells the adhesiveness of integrins is spatially and temporally regulated so that integrins are activated near the leading edge to support lamellipod extension and deactivated near the trailing edge to support uropod retraction and internalization (Alon and Dustin, 2007; Arnaout et al., 2005; Broussard et al., 2008; Calderwood, 2004; Evans and Calderwood, 2007; Luo et al., 2007).
Integrin αIIbβ3, the most abundant receptor on platelets, binds to fibrinogen and von Willebrand factor, and mediates platelet aggregation and association with injured vessel walls. Inherited mutations in its αIIb or β3 subunits result in the bleeding disorder Glanzmann's thrombasthenia. RGD-mimetic small molecules and an antibody to αIIbβ3 are prescribed for the prevention of thrombosis ((Springer et al., 2008; Xiao et al., 2004).
The integrin α and β subunits have large N-terminal extracellular domains, single-pass transmembrane domains, and usually short C-terminal cytoplasmic domains. The first crystal structure of an integrin ectodomain, of αVβ3, represented a huge advance (Xiong et al., 2001; Xiong et al., 2002). Together with subsequent work, ten of twelve domains in the ectofragment were revealed in a bent conformation (Xiao et al., 2004; Xiong et al., 2004). A ligand-binding head formed by both subunits is followed by legs in each subunit that connect to the transmembrane domains. There is an extreme bend at knees between the upper and lower legs. Integrin epidermal growth factor-like (I-EGF) domains 1 and 2 at the β-knee were disordered in the previous αVβ3 structure. Crystals of β2 leg fragments containing I-EGF domains 1 and 2 have been solved in two different orientations (Shi et al., 2007), but the conformation of these domains in the bent integrin conformation remains unknown.
Subsequent to the αVβ3 crystal structure, mutational studies on cell surface integrins and EM studies on αVβ3, αLβ2, and αXβ2 integrins demonstrated that the bent conformation is the physiologically relevant, low affinity integrin conformation (Nishida et al., 2006; Takagi et al., 2002). Nonetheless, a cryo EM study on αIIbβ3 revealed a different, less compact conformation with a different arrangement of leg domains (Adair and Yeager, 2002). Furthermore, two recent studies have revealed extended conformations of αIIbβ3 but failed to find a bent conformation (Rocco et al., 2008; Ye et al., 2008). Crystal structure studies on αIIbβ3 are important to resolve these controversies. Revealing the structure within a complete ectodomain of the bent β-knee is important to understanding the mechanism of integrin extension. Moreover, no integrin crystal structure to date has described the bent structure in the light of current knowledge that it is physiologically relevant, is in a low-affinity state, and with the aim of understanding how the bent conformation is stabilized and how it transitions to extended conformations. The previous αVβ3 bent conformation was described as “not expected to occur in the membrane-bound receptor,” and being in “its active (ligand competent) state” (Xiong et al., 2001).
Most studies find that upon activation, integrins extend. Upon extension, the headpiece can remain in the closed conformation, as when bent, or transition to an open conformation with high affinity for ligand (Xiao et al., 2004). In contrast, a “deadbolt model” posits that activation can occur in the absence of extension (Arnaout et al., 2005). Binding of cytoskeletal proteins such as talin and kindlins to the integrin β cytoplasmic domain appears to interfere with α/β cytoplasmic domain association, and induce integrin extension (Wegener and Campbell, 2008). However, there is currently no known feature of integrin structure that would enable cytoskeleton binding to couple to the extended, open conformation with high affinity for ligand. This would appear to be important to fulfill the key role of integrins in integrating the extracellular and intracellular environments.
Three closely linked metal ion binding sites in the β I domain are especially important in ligand binding. Mg2+ at the central, metal ion-dependent adhesion site (MIDAS) site directly coordinates the acidic sidechain shared by all integrin ligands. However, in previous unliganded, bent αVβ3 structures, the MIDAS and one adjacent site were unoccupied, and it was proposed that metal binding was either caused by integrin activation or induced by ligand binding (Xiong et al., 2002) However, crystals have not been reported with a combination of the two metal ions important for integrin ligand binding, Mg2+ and Ca2+. Therefore, in current comparisons between low and high affinity β I domain conformations, the changes associated with ligand binding and metal binding cannot be deconvoluted.
SUMMARY OF THE CLAIMS
The methods described herein are based in part on the discovery that a disulfide bond can be introduced to an integrin polypeptide by the substitution of at least one cysteine residue in the polypeptide. The disulfide bond(s) formed in the integrin polypeptide stabilize the integrin in a “closed/inactive” state, which permits the integrins to be screened for a candidate molecule that can bind to the closed state. In particular, this approach can be used to screen for agents that bind to the closed state of an integrin polypeptide, and would be useful as therapeutic treatments to prevent integrin activation.
In one aspect, the methods described herein relate to a method of identifying a candidate modulator of integrin activity, comprising (a) contacting an integrin polypeptide with a candidate agent, wherein the integrin polypeptide is locked into a desired conformation; and (b) detecting binding of the candidate agent to the integrin polypeptide, wherein binding of the candidate agent to the integrin polypeptide is indicative that the candidate agent is a candidate modulator of integrin activity.
In one embodiment of this aspect and all other aspects described herein, The method of the candidate agent is selected from the group consisting of an antibody, a small molecule, a chemical, a peptide, and a peptidomimetic.
In another embodiment of this aspect and all other aspects described herein, the candidate modulator stabilizes the integrin polypeptide into a closed conformation. Alternatively, the candidate modulator can induce a conformational shift from the open conformation to the closed conformation.
In another embodiment of this aspect and all other aspects described herein, the candidate modulator inhibits binding of an integrin ligand to the integrin polypeptide. Alternatively, the candidate modulator may act at a site distant from the integrin ligand site to prevent integrin-mediated activity in response to ligand binding—that is, ligand binding may occur but activation of the integrin activity is blocked (e.g., non-competitive inhibition).
In another embodiment of this aspect and all other aspects described herein, the integrin polypeptide is selected from the group consisting of αVβ3, αIIbβ3, αVb6, αVβ1, αVβ5, αMβ2, αXβ2, αLβ2, and αVβ8.
In another embodiment of this aspect and all other aspects described herein, wherein locking the integrin polypeptide into the desired conformation comprises introducing a stabilizing disulfide bond into the integrin polypeptide.
In another embodiment of this aspect and all other aspects described herein, the disulfide bond is formed by a cysteine residue substitution of at least one amino acid residue of said integrin polypeptide.
In another embodiment of this aspect and all other aspects described herein, the substitution comprises a mutation selected from the group consisting of: L959C (human αIIb), E960C (human αIIb), 1955C (human αV), Q956C (human αV), V664C (human β3), P688C (human β3), L662C (human β6), P686C (human β6), A619C (human β8), and F636C (human β3).
In another embodiment of this aspect and all other aspects described herein, the candidate agent is further assayed for activation or inhibition of integrin activity. In one embodiment, a cell-based assay is used to determine integrin activity.
Another aspect described herein is an integrin polypeptide composition stabilized in the “closed” conformation. In one embodiment, the integrin polypeptide is stabilized by substitution of at least one amino acid residue for a cysteine residue, wherein a disulfide bond is formed.
In another embodiment of this aspect and all other aspects described herein, the substitution comprises a mutation selected from the group consisting of: L959C (human αIIb), E960C (human αIIb), 1955C (human αV), Q956C (human αV), V664C (human β3), P688C (human β3), L662C (human β6), P686C (human β6), A619C (human β8), and F636C (human β3).
In another embodiment of this aspect, the composition further comprises a solid support such as a bead, a dish, a well, a plate, etc.
DEFINITIONS
As used herein, a “modified integrin I-domain polypeptide” or “modified integrin polypeptide” includes an integrin I-domain polypeptide that has been altered with respect to the wild-type sequence or the native state such that at least one disulfide bond has been introduced into the polypeptide thereby stabilizing the integrin in a desired conformation. An integrin polypeptide is considered “locked into a desired conformation” if the disulfide bond prevents a conformational shift in the integrin polypeptide from occurring under non-denaturing conditions (i.e., denaturing conditions can be induced by e.g., high temperatures, the presence of reducing agents (such as β-mercaptoethanol, dithiothreitol), the presence of strong denaturing reagents (such as 6M guanidinium hydrochloride, 8M urea, or 1% sodium dodecyl sulfate), or any combination thereof).
As used herein, the term “stabilizing disulfide bond” is used to describe substitution of at least one cysteine residue that permits the formation of a disulfide bond, which in turn prevents a conformational shift in the integrin polypeptide even in the presence of an activating ligand. The “stabilizing disulfide bond” is introduced to the polypeptide by one of skill in the art and does not reflect a natural or native disulfide bond of the polypeptide. However, it is contemplated that an integrin polypeptide with such a stabilizing disulfide bond can be found in nature due to a mutation in amino acid sequence.
As used herein, the term “binding of the candidate agent” refers to an interaction of a candidate agent with an integrin polypeptide stabilized in a closed conformation. Since the conformation of the integrin polypeptide is held in place by a disulfide bond, the term “binding” reflects an interaction and is insufficient to indicate the inhibitory or activating activity of the compound. Further screening assays for integrin activity, as described herein, should be used to determine the action of a candidate agent.
As used herein, the term “candidate agent” includes a compound or other agent that is capable of at least binding to an integrin polypeptide or modified polypeptide as described herein. In an alternative embodiment, the compound or agent is “a modulator of integrin activity,” which is capable of modulating or regulating at least one integrin activity, as described herein. Modulators of integrin activity may include, but are not limited to, small organic or inorganic molecules, nucleic acid molecules, peptides, antibodies, and the like. A modulator of integrin activity can be an inducer or inhibitor of integrin-mediated activities such as cell adhesion or ligand binding. As used herein, an “inducer of integrin activity” stimulates, enhances, and/or mimics an integrin activity. As used herein, an “inhibitor of integrin activity” reduces, blocks or antagonizes an integrin activity.
As used interchangeably herein, the terms “integrin activity”, or “integrin-mediated activity” refer to an activity exerted by an integrin polypeptide or nucleic acid molecule on an integrin responsive cell, or on integrin ligand or receptor, as determined in vitro and in vivo, according to standard techniques. In one embodiment, an integrin activity is the ability to mediate cell adhesion events, e.g., cell to cell, or cell to extracellular matrix adhesion. In another embodiment, an integrin activity can be measured as the ability to transduce cellular signaling events. In yet another embodiment, an integrin activity is the ability to bind a ligand, e.g., ICAM.
As used herein, the term “inhibition of integrin activity” refers to a decrease in ligand activated integrin activity of at least 10% as assessed using a cell-based integrin assay; preferably the activity of the integrin is decreased by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or even 100% (i.e., no activity) integrin activity in the same cell-based integrin assay.
As used herein, the term “inhibition of integrin activity” refers to a decrease in ligand activated integrin activity of at least 10% as assessed using a cell-based integrin assay; preferably the activity of the integrin is decreased by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or even 100% (i.e., no activity) integrin activity in the same cell-based integrin assay.
As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the invention, yet open to the inclusion of unspecified elements, whether essential or not.
As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the invention.
The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows disulfide bond formation in mutant receptors and effect on function. 293T cells were co-transfected with full-length, wild-type or mutant integrin subunits to express the indicated α/β pairs on the cell surface. A. Integrin heterodimers were immunoprecipitated from 35S-labeled cell detergent lysates with anti-β3 mAb AP3 and subjected to non-reducing SDS-PAGE and fluorography. Molecular size markers are shown on the left. B. Soluble fibrinogen binding to 293T transfectants in the presence of 1 mM Ca2+/1 mM Mg2+ (white) or 1 mM Mn2+ plus 10 mg/ml PT25-2 antibody (black). Binding was measured as the mean fluorescence intensity of FITC-conjugated fibrinogen staining as a percentage of mean fluorescence intensity of staining with Cy3-conjugated AP3 mAb. Methods were as described previously (Luo, et al. 2004; Zhu, et al. 2007).
FIG. 2 show disulfide formation efficiency of the αLβ2 cys mutants on cell surface. The lane numbers in the left panel correspond to the combination of αL and β2 subunits connected by lines shown in the right panel. #1 was not well expressed in this particular experiment. FIG. discloses SEQ ID NOS 104 and 81, respectively, in order of appearance.
FIG. 3 shows expression level of disulfide locked αLβ2 mutants on 293T cell surface.
FIG. 4 shows exemplary LFA-1 disulfide mutants on 293T cell.
FIGS. 5A-5C show LFA-1 crosslinking on cell surface. FIG 5A. Sequences around the cysteine mutations are shown (SEQ ID NOS 85-94, respectively, in order of appearance). Cysteine mutations were introduced and are shown, and the names of each exemplary construct are labeled at the right. FIG. 5B. Expression of the tested α/β combinations was tested using a FACS assay to identify cell surface expression. Disulfide bond formation was detected by Western blotting of lysed cell after transfection. FIG. 5C. A schematic representation of the α/β combinations tested and shown in FIG. 2B (SEQ ID NOS 104 and 81, respectively, in order of appearance).
FIGS. 6A-6C show soluble integrin αLβ2 (LFA-1) and αXβ2 (CR4) crosslinking and activation. FIG. 6A. C-terminal sequence of constructs used for soluble integrin expression (SEQ ID NOS 95-103, respectively, in order of appearance). The cysteine mutations were introduced and are shown. The name of each construct is depicted at the right of each sequence. Tags and other features are labeled above the sequences. His6 tag disclosed as SEQ ID No: 105. FIG. 6B. Exemplary α/β combinations were tested in transfection and protein purification experiments. Crosslinking was confirmed by SDS-PAGE after protein purification and TEV cleavage. FIG 6C. Activation status of purified integrin proteins was monitored by KIM127 exposure in 1 mM Ca2+/Mg2+.
FIG. 7 shows optimal sequence alignments of exemplary integrin alpha subunits. FIG. 7 includes a sequence alignment of AV_HU—4504763 (SEQ ID NO: 1), AV_MO—6680486 (SEQ ID NO: 2), A5_HU—124946 (SEQ ID NO: 3), A5_MO—6754378 (SEQ ID NO:4), AB_HU—124951 (SEQ ID NO: 5), AB_MO—12643835 (SEQ ID NO: 6), A8_HU—1708570 (SEQ ID NO: 7), A6_HU—4557675 (SEQ ID NO: 8), A6_MO—7110659 (SEQ ID NO: 9), A7_HU—4504753 (SEQ ID NO: 10), A7_MO1—3378244 (SEQ ID NO: 11), A7_MO2—3378244 (SEQ ID NO: 12), A3_HU-11467963 (SEQ ID NO: 13), A3_MO—7305189 (SEQ ID NO: 14), A4_HU—4504749 (SEQ ID NO: 15), A4_MO—7110657 (SEQ ID NO: 16), A9_HU—2833247 (SEQ ID NO: 17), A1_HU—2829468 (SEQ ID NO: 18), A2_HU—4504743 (SEQ ID NO: 19), A2_MO—6680478 (SEQ ID NO: 20), A10_HU—6650628 (SEQ ID NO: 21), A11_HU—12643894 (SEQ ID NO: 22), AE—1HU—6007851 (SEQ ID NO: 23), AE_MO—6680482 (SEQ ID NO: 24), AD_HU—12643717 (SEQ ID NO: 25), AX_HU—4504765 (SEQ ID NO: 26), AX_MO—10946646 (SEQ ID NO: 27), AM_HU—1708572 (SEQ ID NO: 28), AM_MO—124956 (SEQ ID NO: 29), AL_HU—1170591 (SEQ ID NO: 30), and AL_MO—124953 (SEQ ID NO: 31).
FIG. 8 shows optimal sequence alignments of exemplary integrin beta subunits. FIG. 8 includes a sequence alignment of sequences B1_HUMAN—4504767 (SEQ ID NO: 32), B1_MOUSE—124964 (SEQ ID NO: 33), B2_HUMAN—14780741 0332-H (SEQ ID NO: 34), B2_MOUSE—3183523 (SEQ ID NO: 35), B3_HUMAN—2119640 (SEQ ID NO: 36), B3_MOUSE—7949057 (SEQ ID NO: 37), B4_HUMAN—14768997 (SEQ ID NO: 38), B4_MOUSE—484-472 (SEQ ID NO: 39), B5_HUMAN—106776 (SEQ ID NO: 40), B5_MOUSE—3478697 y236-C (SEQ ID NO: 41), B6_HUMAN—9625002 (SEQ ID NO: 42), B6_MOUSE—10946686 (SEQ ID NO: 43), B7_HUMAN—4504777 (SEQ ID NO: 44), B7_MOUSE—7305193 (SEQ ID NO: 45), B8_HUMAN—4504779 (SEQ ID NO: 46), and PACTOLU_MOUSE—3287491 (SEQ ID NO: 47). “SNTT”disclosed as residues 646-649 of SEQ ID NO: 47.



DETAILED DESCRIPTION
The methods described herein are based in part on the discovery that the introduction of a disulfide bond into an integrin polypeptide by the substitution of at least one cysteine residue in the polypeptide permits stabilization of the integrin in a “closed/inactive” state. This stabilizing disulfide bond permits integrins to be screened for a candidate molecule that can bind to the closed state. In particular, this approach can be used to screen for agents that bind to the closed state of an integrin polypeptide, and would be useful as therapeutic treatments to prevent integrin activation.
The αIIbβ3 crystal structure. A crystal structure for molecule I in αIIbβ3 crystals was determined and ribbon diagrams were prepared (data not shown). The following characteristics are noted. In one model, the αIIbβ3 is extended by torsion at the α and β-knees. Upon supersition of molecules 1 and 2 of αIIbβ3 and αVβ3 (Xiong et al., 2004) the structures indicate “breathing”. It is determined that there is a variation in the distance of the lower α-leg from the lower β-leg, opening its cleft, and variation in the lower β-leg: αIIbβ3 molecule 1 and αVβ3. A view of the α-subunit only rotated about 90° indicates variation in the distance of the lower α-leg from the upper α-headpiece: αIIbβ3 molecule 1 and molecule 2; αVβ3. The headpieces of αIIbβ3 molecule 1 and αVβ3 show breathing at the β I/hybrid domain interface. Further information regarding the solved crystal structure for the αIibβ3 integrin can be found in a published paper by the inventors (Zhu, et al., Molecular Cell (2008) 32(6): 849-862).

Disulfide Bonds

Disulfide bond formation occurs between two cysteine residues that are appropriately positioned within the three-dimensional structure of an integrin polypeptide. In one embodiment of the invention, a polypeptide is stabilized in the closed conformation by introducing at least one cysteine substitution into the amino acid sequence such that a disulfide bond is formed. The introduction of a single cysteine substitution is performed in circumstances in which an additional cysteine residue is present in the native amino acid sequence of the polypeptide at an appropriate position such that a disulfide bond is formed. Alternatively, in another embodiment, two cysteine substitutions are introduced into the amino acid sequence of the polypeptide at positions that allow a disulfide bond to form, thereby stabilizing the polypeptide in a desired conformation.
In one embodiment of the invention, cysteine substitutions are introduced such that the formation of a disulfide bond is favored only in one protein conformation (i.e., a closed conformation), such that the protein is stabilized in that particular conformation.
Preparation of a modified Polypeptide of the invention by introducing cysteine substitutions can be achieved by mutagenesis of DNA encoding the integrin polypeptide of interest. For example, an isolated nucleic acid molecule encoding a modified integrin I-domain polypeptide can be created by introducing one or more nucleotide substitutions into the nucleotide sequence of an integrin gene such that one or more amino acid substitutions, e.g., cysteine substitutions, are introduced into the encoded protein. Mutations can be introduced into a nucleic acid sequence by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis.
Some non-limiting examples of substituted cysteine residues in α/β subunits include the following and are denoted with a bold, underlined C:












Subunit







Human αIIb
946
RGEAQVWTQLLRACEERA-
963
(SEQ ID NO: 48);


 


Human αIIb
946
RGEAQVWTQLLRALCERA-
963
(SEQ ID NO: 49);


 


Human αv
942
TNSTLVTTNVTWGCQPAPM
960
(SEQ ID NO: 50);


 


Human αv
942
TNSTLVTTNVTWGICPAPM
960
(SEQ ID NO: 51);


 


Human β3
663
CCVRFQYYEDSS--GKSILYVVEEPECPKG
690
(SEQ ID NO: 52);


 


Human β3
663
CVVRFQYYEDSS--GKSILYVVEEPECCKG
690
(SEQ ID NO: 53);


 


Human β6
661
CCITFLITTDNE--GKTIIHSINEKDCPKP
688
(SEQ ID NO: 54);


 


Human β6
661
CLITFLITTDNE--GKTIIHSINEKDCCKP
688
(SEQ ID NO: 55);


 


Human β8
619
CCLMEQQ-----------HYVDQTSECFSS
637
(SEQ ID NO: 56);


 


and






 


Human β8
619
CALMEQQ-----------HYVDQTSECCSS
637
(SEQ ID NO: 57).






In another embodiment, the method of the invention can be used to stabilize a protein in a biologically inactive conformation, e.g., a conformation that is enzymatically inactive or does not have ligand binding capacity and/or effector functions, e.g., a “closed” conformation.
Proteins that are stabilized in a particular conformation find use in, for example, in proteomic screening technologies. In proteomic screens of tissues and disease states, antibodies, polypeptide, and/or small molecules that are specific for, e.g., an inactive protein conformer, can be used to assess the activity of different cellular signaling, metabolic, and adhesive pathways. Thus, associations can be made between specific diseases and the activation of specific biochemical and signaling pathways. Furthermore, the methods described herein relate to polypeptides, antibodies, and small molecules identified using the methods described herein and uses for same, e.g., to treat, for example, inflammatory disorders. Conformer-specific reagents can also be placed on chips and used to screen tissue extracts, or used to stain tissue sections. Furthermore, drugs or antibodies, e.g., anti-integrin antibodies which specifically recognize a modified integrin I-domain polypeptide, e.g., an anti-LFA-1 antibody which specifically recognizes a modified LFA-1 I-domain polypeptide, that are selective for a particular conformer, e.g., an open conformer or a closed conformer, may provide differential therapeutic effects. Therefore, selective screening assays using a protein stabilized in a particular conformer can be used to rationally obtain compounds with a desired activity.
Integrins
Integrins, exist on cell surfaces in an inactive conformation that does not bind ligand. Upon cell activation, integrins change shape (conformation) and can bind ligand. Over 20 different integrin heterodimers (different α and β subunit combinations) exist that are expressed in a selective fashion on all cells in the body. After activation, integrins bind in a specific manner to protein ligands on the surface of other cells, in the extracellular matrix, or that are assembled in the clotting or complement cascades. Integrins on leukocytes are of central importance in leukocyte emigration and in inflammatory and immune responses. Ligands for the leukocyte integrin Mac-1 (αMβ2) include the inflammation-associated cell surface molecule ICAM-1, the complement component iC3b, and the clotting component fibrinogen. Ligands for the leukocyte integrin LFA-1 (αLβ2) include ICAM-1, ICAM-2, and ICAM-3. Antibodies to leukocyte integrins can block many types of inflammatory and auto-immune diseases, by, e.g., modulating, or inhibiting, for example, cell to cell interactions, or cell to extracellular matrix interactions. Integrins on platelets are important in clotting and in heart disease and approved drugs that interact with platelet integrin function include the antibody abciximab (ReoproTM) and the peptide-like antagonist eptifibatide (IntegrilinTM). Integrins on connective tissue cells, epithelium, and endothelium are important in disease states affecting these cells. They regulate cell growth, differentiation, wound healing, fibrosis, apoptosis, and angiogenesis. Integrins on cancerous cells regulate invasion and metastasis.
It is contemplated herein that an agent can be used to bind to integrins in the “closed conformation” in order to stabilize integrins in their off state and modify or prevent integrin activation.
One embodiment of the methods described herein provides a modified integrin I-domain polypeptide comprising at least one disulfide bond, such that the modified I-domain polypeptide is stabilized in a desired conformation. A modified integrin I-domain polypeptide of the invention may be derived from an I-domain of an integrin a subunit including α1, α2, α10, α11, αD, αV, αX, αM, αE, αL (CD11a), αM (CD11b) and αX (CD11c).
Also contemplated herein are integrins with conservative substitutions. Conservative substitutions (substituents) typically include the substitution of one amino acid for another with similar characteristics (e.g., charge, size, shape, and other biological properties) such as substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. The non-polar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. It is also contemplated herein that a substitution can occur among amino acid groups with varying characteristics.
In other embodiments, derivatives with amino acid substitutions which are less conservative may also result in desired derivatives, e.g., by causing changes in charge, conformation and other biological properties. Such substitutions would include, for example, substitution of a hydrophilic residue for a hydrophobic residue, substitution of a cysteine or proline for another residue, substitution of a residue having a small side chain for a residue having a bulky side chain or substitution of a residue having a net positive charge for a residue having a net negative charge. When the result of a given substitution cannot be predicted with certainty, the derivatives may be readily assayed according to the methods disclosed herein to determine the presence or absence of the desired characteristics. The polypeptides and proteins as described herein may also be modified by various changes such as insertions, deletions and substitutions, either conservative or nonconservative where such changes might provide for certain advantages in their use.
In a preferred embodiment, a cysteine residue is substituted into the integrin polypeptide to permit the formation of a disulfide bond. In one embodiment, a modified integrin I-domain polypeptide of the invention is encoded by an amino acid sequence containing at least one cysteine substitution, or alternatively two cysteine substitutions, as compared to the wild-type sequence.
The introduction of cysteine residues at appropriate positions within the amino acid sequence of the I-domain polypeptide allows for the formation of a disulfide bond that stabilizes the domain in a particular conformation, e.g., an inactive “closed” conformation. For example, the αL L289C/K294C mutant and the αM Q163C/R313c mutants are stabilized in an inactive or “closed” conformation that does not bind ligand.
In one embodiment, described herein is a modified integrin I-domain which is comprised within an integrin subunit, and which may be further associated with an integrin β subunit. In another embodiment, a modified integrin I-domain polypeptide of the invention is a soluble polypeptide. Furthermore, the invention provides a modified integrin I-domain polypeptide which is operatively linked to a heterologous polypeptide. Modified integrin polypeptides of the invention include modified integrin I-domain and I-like domain polypeptides that are comprised within an integrin α or β subunit polypeptide, respectively; soluble modified integrin I-domain and I-like domain polypeptides; and modified integrin I-domain and I-like domain polypeptides that are operatively linked to a heterologous polypeptide, e.g., fusion proteins.
Some non-limiting examples of substituted cysteine residues in α/β subunits include the following and are denoted with a bold, underlined C:












Subunit







Human αIIb
946
RGEAQVWTQLLRACEERA-
963
(SEQ ID NO: 48);


 


Human αIIb
946
RGEAQVWTQLLRALCERA-
963
(SEQ ID NO: 49);


 


Human αv
942
TNSTLVTTNVTWGCQPAPM
960
(SEQ ID NO: 50);


 


Human αv
942
TNSTLVTTNVTWGICPAPM
960
(SEQ ID NO: 51);


 


Human β3
663
CCVRFQYYEDSS--GKSILYVVEEPECPKG
690
(SEQ ID NO: 52);


 


Human β3
663
CVVRFQYYEDSS--GKSILYVVEEPECCKG
690
(SEQ ID NO: 53);


 


Human β6
661
CCITFLITTDNE--GKTIIHSINEKDCPKP
688
(SEQ ID NO: 54);


 


Human β6
661
CLITFLITTDNE--GKTIIHSINEKDCCKP
688
(SEQ ID NO: 55);


 


Human β8
619
CCLMEQQ-----------HYVDQTSECFSS
637
(SEQ ID NO: 56);


 


and






 


Human β8
619
CALMEQQ-----------HYVDQTSECCSS
637
(SEQ ID NO: 57).






The cDNAs, for multiple human integrin α and β subunit polypeptides have been cloned and sequenced, and the polypeptide sequences have been determined (see, for example, GenBank Accession Numbers: NM—002203 (α2), AF112345 (α10), NM—012211 (α1), NM—005353 (αD), NM—002208 (αE), NM—000887 (αX), NM—000632 (αM), NM—002209 (αL), X68742 and P56199 (α1), NM000211 (β2), NM—000212 (β3), NM—002214 (β8)). In addition, the sequences encoding integrin α and β subunit polypeptides from other species are available in the art. Furthermore, as described previously, three dimensional structure of the αM, αL, α1 and α2 I-domains has been solved (Lee, J-O, et al. (1995) Structure 3:1333-1340; Lee, J-O, et al. (199S) Cell 80:631-638; Qu, A and Leahy, D J (1995) Proc Natl Acad Sci USA 92:10277-10281; Qu, A and Leahy, D J (1996) Structure 4:931-942; Emsley, Jet al. (1997) J Biol Chem 272:28512-28517; Baldwin, E T et al. (1998) Structure 6:923-935; Kallen, J et al. (1999) J Mol Biol 292:1-9).
Isolated modified integrin polypeptides as described herein preferably have an amino acid sequence that is sufficiently identical to the amino acid sequence of a native integrin polypeptide, yet which comprise at least one, and alternatively two cysteine substitutions, such that a disulfide bond is formed that stabilizes the polypeptide in a desired conformation. As used herein, the term “sufficiently identical” refers to an amino acid (or nucleotide) sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an amino acid residue that has a similar side chain) amino acid residues (or nucleotides) to an integrin amino acid (or nucleotide) sequence such that the polypeptide shares common structural domains or motifs, and/or a common functional activity with a native integrin polypeptide. For example, amino acid or nucleotide sequences which share at least 30%, 40%, or 50%, preferably 60%, more preferably 70%, 75%, 80%, 85% or 90%, 91%, 92%, 93%, 94%, 95% or greater identity and share a common functional activity (e.g., an activity of a modified integrin I-domain or I-like domain as described herein) are defined herein as sufficiently identical. An integrin I-domain polypeptide may differ in amino acid sequence from the integrin polypeptides disclosed herein due to natural allelic variation or mutagenesis.
To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, and even more preferably at least 70%, 80%, or 90% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In one embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available on the world wide web at gcg.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available on the world wide web at gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (Comput. Appl. Biosci., 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
Alternatively, sequences aligned for optimal comparison purposes can be used to find residues that are homologous among a variety of α or β integrin subunits, such that substitution of a cysteine residue known to stabilize an integrin in a closed conformation in one isoform can be extended to another isoform. One of skill in the art can readily align sequences in an optimal manner to determine a preferred site for cysteine substitution. Provided herein are sequences aligned in an optimal manner for the purpose of determining a preferred site for cysteine substitution. For example, mutation sites in αVβ1, and αVβ5 can be determined from alignment with αVβ6 and αVβ8 sequences. Alternatively, mutation sites in αMβ2 can be determined from alignment with the αXβ2 sequence.
In one embodiment, modified integrin polypeptides are produced by recombinant DNA techniques. For example, a modified integrin polypeptide can be isolated from a host cell transfected with a polynucleotide sequence encoding a modified integrin polypeptide (e.g., a I-domain polypeptide or a soluble I-domain fusion protein) using an appropriate purification scheme using standard protein purification techniques. Alternative to recombinant expression, a modified integrin polypeptide can be synthesized chemically using standard peptide synthesis techniques.
Integrins and Disease
Integrins are key targets in many diseases. Accordingly, isolated high affinity I-30 domains of the invention, as well as antibodies, or small molecule antagonists selective for activated leukocyte integrins can be used to modulate, e.g., inhibit or prevent, autoimmune and inflammatory disease, transplant rejection, ischemia/reperfusion injury as in hypovolemic shock, myocardial infarct, and cerebral shock. Furthermore, co-crystals of high affinity I domains bound to natural ligands and/or small molecule antagonists can readily be made, which will enable computational drug design, and advance modification and improvement of drug development candidates.
Accordingly, in one aspect the methods described herein provide a method for identifying a modulator of integrin activity comprising assaying the ability of a test compound to bind to a modified integrin I-domain polypeptide which is stabilized in the closed conformation. In another embodiment, the invention provides a method for identifying a compound capable of modulating the interaction of an integrin and a cognate ligand wherein binding of a ligand to a modified integrin I-domain polypeptide, which is stabilized in the closed conformation, is assayed in the presence and absence of a test compound.
As used herein, an integrin mediated disorder includes, for example, an inflammatory or immune system disorder, and/or a cellular proliferative disorder. Examples of integrin-mediated disorders include myocardial infarction, stroke, restenosis, transplant rejection, graft versus host disease or host versus graft disease, and reperfusion injury. An inflammatory or immune system disorder includes, but is not limited to adult respiratory distress syndrome (ARDS), multiple organ injury syndromes secondary to septicemia or trauma, viral infection, inflammatory bowel disease, ulcerative colitis, Crohn's disease, leukocyte adhesion deficiency II syndrome, thermal injury, hemodialysis, leukapheresis, peritonitis, chronic obstructive pulmonary disease, lung inflammation, asthma, acute appendicitis, dermatoses with acute inflammatory components, wound healing, septic shock, acute glomerulonephritis, nephritis, amyloidosis, reactive arthritis, rheumatoid arthritis, chronic bronchitis, Sjorgen's syndrome, sarcoidosis, scleroderma, lupus, polymyositis, Reiter's syndrome, psoriasis, dermatitis, pelvic inflammatory disease, inflammatory breast disease, orbital inflammatory disease, immune deficiency disorders (e.g., HIV, common variable immunodeficiency, congenital X-linked infantile hypogammaglobulinemia, transient hypogammaglobulinemia, selective IgA deficiency, necrotizing enterocolitis, granulocyte transfusion associated syndromes, cytokine-induced toxicity, chronic mucocutaneous candidiasis, severe combined immunodeficiency), autoimmune disorders, and acute purulent meningitis or other central nervous system inflammatory disorders.
Screening Assays
The methods described herein (also referred to herein as a “screening assay”) can be used to identify modulators, i.e., candidate or test compounds or agents (e.g., peptides, antibodies, peptidomimetics, small molecules (organic or inorganic) or other drugs) which modulate integrin activity. These assays are designed to identify compounds, for example, that bind to an integrin I-domain polypeptide, e.g., an integrin I-domain polypeptide in an active conformation, binds to other proteins that interact with an integrin I-domain polypeptide, induce binding, and modulate the interaction of an integrin I-domain polypeptide with other proteins, e.g., an integrin ligand, e.g., ICAM, and thus modulate integrin activity.
In the case of an integrin stabilized in the closed conformation, a lack of integrin activity indicates that the integrin is stabilized in the “off” position. In order to screen candidate modulators that bind to this particular conformation, it is necessary to measure binding of the candidate agent to the integrin, rather than assessing integrin activity. Binding assays are known in the art and can be achieved using e.g., radioligand binding assays or fluorescence-detected binding. Candidate modulators that are capable of binding an integrin stabilized in a desired conformation will need to be confirmed as an inhibitor or stimulator of integrin activity using an integrin that is not stabilized in a particular confirmation. Integrin activity assays for such purposes are well known in the art and/or are described herein.
In an alternate embodiment, a soluble, recombinant high affinity integrin I-domain can be used to screen for small molecule antagonists that interfere with integrin ligand binding. Furthermore, antagonists, e.g., antibodies, with direct/competitive and indirect/noncompetitive modes of inhibition can be discriminated, based on comparison with effects on wild-type integrin I-domains which show minimal ligand binding activity. For example, an indirect inhibitor should inhibit ligand binding by an activated, wild-type integrin I-domain, but not by a disulfide-locked high affinity I-domain.
In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a modified integrin polypeptide on the cell surface with a test compound and determining the ability of the test compound to modulate (e.g., induce or inhibit) an integrin activity. For example, a cell expressing a modified integrin I-domain polypeptide stabilized in an open conformation on the cell surface is contacted with a test compound, and the ability of the test compound to modulate adhesion to an integrin ligand is determined, as described herein.
In another embodiment, the ability of a test compound to modulate integrin ligand binding can also be determined, for example, by coupling a modified integrin I-domain polypeptide that is stabilized in e.g., an open conformation with a detectable label such that the binding of the modified integrin polypeptide can be determined by detecting the amount of labeled integrin I-domain binding to an immobilized integrin ligand.
Animal-based model systems, such as an animal model of inflammation, may be used, for example, as part of screening strategies designed to identify compounds which are modulators of integrin activity. Thus, the animal-based models may be used to identify drugs, pharmaceuticals, therapies and interventions which may be effective in modulating inflammation and treating integrin-mediated disorders. For example, animal models may be exposed to a compound suspected of exhibiting an ability to modulate integrin activity, and the response of the animals to the exposure may be monitored by assessing inflammatory activity before and after treatment. Transgenic animals, e.g., transgenic mice, which express modified integrin I-domain polypeptides as described herein can also be used to identify drugs, pharmaceuticals, therapies and interventions which may be effective in modulating inflammation and treating integrin-mediated disorders
In another aspect, the methods described herein pertain to a combination of two or more of the assays described herein. For example, a modulator of integrin activity can be identified using a cell-based assay, and the ability of the agent to modulate integrin activity can be confirmed in vivo, e.g., in an animal such as an animal model for inflammation.
Moreover, screening assays can be used to identify inducers of integrin activity, for example, that mimic the activity of a integrin polypeptide, e.g., the binding of an integrin to a ligand or receptor, or the activity of an integrin towards an integrin responsive cell. Such compounds may include, but are not limited to, peptides, antibodies, or small organic or inorganic compounds. An anti-integrin antibody, e.g., an anti-LFA-1 antibody, which selectively binds to an open, activated conformer can be used to assess the ability of a test compound to activate, inactivate, or prevent activation of an integrin.
The test compounds can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the ‘one-bead one-compound’ library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K. S. (1997) Anticancer Drug Des. 12:145).
Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261:1303; Carrell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med. Chem. 37:1233.
Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat. No. '409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA 89:1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310); (Ladner supra.).
The methods described herein further pertain to novel agents identified by the above-described screening assays. With regard to intervention, any treatments which modulate integrin activity and/or inflammatory activity should be considered as candidates for human therapeutic intervention.
Other Embodiments
Reported herein are disulfide bonds between integrin α and β subunits in their C-terminal domains or in the linkers between these C-terminal domains and the transmembrane domain. These disulfides may be used in either intact integrins on the cell surface or truncated extracellular domain fragments. The results with disulfide bonds introduced into cell surface integrins are predictive of those that can be successfully introduced into extracellular domain fragments.
Also shown herein are disulfide bonds that stabilize integrins in the bent, low affinity conformation. The stabilized integrins bind ligands and ligand-mimetic Fab less well. The stabilized integrins have utility for screening for conformation-dependent antibodies and drug molecules. Antibodies and drugs may be identified that are selective for the active, non-bent, or inactive, bent integrins, using either cell surface integrins or extracellular domain fragments.
In addition, stabilized integrins on cells, in comparison with wild-type integrins, can be used to select for antibodies selective for the bent, inactive conformation or extended, active conformation. Alternatively, stabilized and wild-type ectodomain integrin fragments can be used to screen for drugs selective for the bent inactive conformation. Such drugs would bind to and stabilize the bent, inactive conformation, but not the extended, active conformation. Thus they would represent a novel class of non-competitive integrin antagonists.
The present invention may be as described in any one of the following numbered paragraphs.

    1. A method for identifying a candidate modulator of integrin activity, the method comprising (a) contacting an integrin polypeptide with a candidate agent, wherein the integrin polypeptide is locked into a desired conformation; and (b) detecting binding of the candidate agent to the integrin polypeptide, wherein binding of the candidate agent to the integrin polypeptide is indicative that the candidate agent is a candidate modulator of integrin activity.
    2. The method of paragraph 1, wherein the candidate agent is selected from the group consisting of an antibody, a small molecule, a chemical, a peptide, and a peptidomimetic.
    3. The method of paragraph 1 or 2, wherein the candidate modulator stabilizes the integrin polypeptide into a closed conformation.
    4. The method of paragraphs 1, 2, or 3 wherein the candidate modulator inhibits binding of an integrin ligand to the integrin polypeptide.
    5. The method of any one of paragraphs 1-4, wherein the integrin polypeptide is selected from the group consisting of αVβ3, αIIbβ3, αVb6, αVβ1, αVβ5, αMβ2, αXβ2, αLβ2, and αVβ8.
    6. The method of any one of paragraphs 1-5, wherein locking the integrin polypeptide into the desired conformation comprises introducing a stabilizing disulfide bond into the integrin polypeptide.
    7. The method of any one of paragraphs 1-6, wherein the disulfide bond is formed by a cysteine residue substitution of at least one amino acid residue of the integrin polypeptide.
    8. The method of any one of paragraphs 1-7, wherein the substitution comprises a mutation selected from the group consisting of: L959C (human αIIb), E960C (human αIIb), 1955C (human αV), Q956C (human αV), V664C (human β3), P688C (human β3), L662C (human β6), P686C (human β6), A619C (human β8), and F636C (human β3).
    9. The method of any one of paragraphs 1-8, wherein an optimal sequence alignment is used to identify homologous residues for a cysteine substitution in an integrin polypeptide selected from the group consisting of αVβ3, αIIbβ3, αVb6, αVβ1, αVβ5, αMβ2, αXβ2, αLβ2, and αVβ8.
    10. The method of any one of paragraphs 1-9, wherein the candidate agent is assayed for activation or inhibition of integrin activity.
    11. The method of any one of paragraphs 1-10, wherein a cell-based assay is used to determine integrin activity.
    12. An integrin polypeptide composition comprising: a modified integrin polypeptide, wherein the integrin polypeptide is locked in a closed conformation.
    13. The composition of paragraph 12, wherein the integrin polypeptide is modified by substitution of at least one amino acid residue for a cysteine residue, whereby a disulfide bond is formed.
    14. The composition of paragraph 12 or 13, wherein the substitution comprises a mutation selected from the group consisting of: L959C (human αIIb), E960C (human αIIb), 1955C (human αv), Q956C (human αV), V664C (human β3), P688C (human β3), L662C (human β6), P686C (human β6), A619C (human β8), and F636C (human β3).


EXAMPLES
Example 1
Structure of a Complete Integrin Ectodomain
Herein the inventors describe a crystal structure of platelet integrin αIIbβ3 in the bent conformation useful for screening for agents that bind to the integrin in its bent conformation. Crystals in Ca2+ and Mg2+ show that physiologically in the low affinity state the metal binding sites in the β I domain are fully occupied. Of two different αIIbβ3 molecules in the asymmetric unit, one has density for all integrin domains. Thus, the conformation in the bent state is revealed of I-EGF domains 1 and 2 at the β-knee, at the epicenter of conformational change. The overall structure, the linkages between domains, the arrangement of the legs within the bent structure, and the effect of hybrid domain swing-out on affinity for ligand, have profound implications for the mechanism of integrin activation. Use of this information in models of extended integrins experiencing forces at sites of cell adhesion reveals how integrin affinity is regulated by force exerted parallel to the membrane by a motile actin cytoskeleton. Integrin structure and mechanochemistry provides a natural mechanism for increasing integrin affinity upon cytoskeleton attachment and decreasing it upon cytoskeleton disassembly.
αIIbβ3 Crystal Structure and Negative Stain EM
A 2.55 Å resolution crystal structure of the complete αIIbβ3 ectodomain in Ca2+ and Mg2+ has been refined to an Rfree of 26.8% (FIG. 1A, Table 1). In comparisons to αVβ3 below, differences in resolution and refinement should be kept in mind. The 3.1 Å αVβ3 structure is refined to an Rfree of 36.7% (Xiong et al., 2004). αIIbβ3 has 95% and 0.4% residues in favored and outlier Ramachandran regions, respectively, and geometry in the 98th percentile (where 100 is the best); whereas αVβ3 has 76% and 6.7% residues in favored and outlier regions, respectively, and geometry in the 21st percentile; all values are as reported by MOLPROBITY (Davis et al., 2007). Water molecules, which have important roles in protein structures such as in forming hydrogen bonds and metal coordinations, have been added to the αIIbβ3 but not to the αVβ3 structure, as appropriate for their respective resolutions. No cis-prolines are present in the αVβ3 structure, whereas 6 are present in the αIIbβ3 structure. Two of the cis-prolines, Pro-163 and Pro-169, are in the ligand-binding β3 I domain. The region around cis-Pro-169 has an electron density typical for the αIIbβ3 structure. There is a shift in the sequence-to-structure register between αVβ3 and αIIbβ3 at β3 167-176, in the specificity-determining loop that forms the outer rim of the ligand-binding pocket in the β3 I domain. Thus, with its higher resolution and better refinement, the αIIbβ3 structure provides details about backbone conformation, hydrogen bonding, and side-chain packing that are important for understanding ligand and metal binding; and for accurate molecular dynamics simulations and structure-guided mutagenesis. Furthermore, for the first time, the structure factors for an integrin ectodomain have been deposited, opening access to the experimental electron density upon which the atomic models are based.
Overall bent structure. The overall arrangement of domains in the two independent αIIbβ3 molecules in the crystal asymmetric unit is similar to that seen in αVβ3 crystals (FIG. 1C), except for differences in angles between domains described below that give insights into breathing. A similar bent conformation in solution in physiologic divalent cations is seen for three distinct αIIbβ3 constructs in negative stain EM with class averaging (FIG. 1F-H). The bent integrins from the three types of constructs are indistinguishable from one another (FIG. 1F panels 1-3, G panels 1-2, H panels 1-4) and show excellent cross-correlation with the αIIbβ3 crystal structure (FIG. 1F panels 1 and 5, G panels 1 and 5, and H, panels 1, 5 and 6). One construct was clasped by appending to the α and β ectodomain C-termini 15-residue linkers containing TEV protease sites, followed by ACID and BASE peptides that associate in an α-helical coiled-coil (Nishida et al., 2006). Association near the C-termini of the α and β subunit ectodomains that is provided in vivo by the association between the αIIb and β3 transmembrane domains (Luo et al., 2004) is mimicked by the clasp (Takagi et al., 2002). The clasped αIIbβ3 particles were 64% bent and 32% extended (with 4% unclassified) (FIG. 1F). Unclasped particles, in which the clasp was removed with TEV protease, were 44% bent and 52% extended (FIG. 1G). A third construct, which was identical to that used in crystallization, contained cysteines introduced in C-terminal portions of the αIIb and β3 subunits in positions that resulted in efficient disulfide bond formation in cell surface integrins (FIG. 2). These mutations, αIIb-L959C and β3-P688C, stabilized the integrin in a bent, closed conformation that closely mimics the bent, closed conformation seen in the clasped and unclasped constructs that lack this disulfide. The disulfide-bonded construct was 100% bent (FIG. 1H).
The differing proportion of bent particles in the three preparations shows that tighter association near the C-termini correlated with maintenance of the bent conformation, and also, with resistance to activation on the cell surface (FIG. 2). This is in agreement with work on other soluble integrin preparations, and a large body of work on cell surface integrins, which has shown that association of the α and β subunit transmembrane and cytoplasmic domains stabilizes integrins in the low-affinity state and in the bent conformation (Luo et al., 2007).
Similar bent conformations have previously been described in EM studies of the resting states of αVβ3, αXβ2, and αLβ2 (Nishida et al., 2006; Takagi et al., 2002). Furthermore, extensive studies using mutations and antibodies to ligand-induced binding sites show that αIIbβ3 is compact on the cell surface when resting, and extended when activated (Honda et al., 1995; Luo et al., 2007). The similarity in packing of two independent examples of αIIbβ3 and of αVβ3 in crystal lattices and similar appearance of multiple soluble integrins in EM, together with the work cited above, strongly suggests that the bent crystal structure determined here is representative of the resting state of most, if not all, integrins. However, three cryo EM, EM, and hydrodynamic studies of detergent soluble αIIbβ3 from platelets have reached conclusions that are incompatible with one another, and with the domain arrangement seen here (Adair and Yeager, 2002; Rocco et al., 2008; Ye et al., 2008). The difficulty in obtaining a consensus view on αIIbβ3 structure may reflect the delicate equilibrium between bent and extended structures (FIG. 1G-H), averaging over ensembles of bent and extended conformations, the poor association of the αIIb and β3 transmembrane domains in detergent (Wegener and Campbell, 2008), and the ease with which the αIIb and β3 subunits dissociate, even on the platelet surface (Luo et al., 2003).
Conceptual advances since the previously described αVβ3 crystal structures allow us to describe the bent αIIbβ3 crystal structure in light of its physiological relevance as the low affinity integrin state, and as the starting point for integrin extension. Furthermore, the αIIbβ3 structure reveals I-EGF domains 1 and 2, and a highly acute bend between them in the bent conformation. In contrast, I-EGF domains 2, 3, and 4 extend in an almost straight orientation, with an approximate 90° left-handed twist between successive domains, to cover most of the length of the lower β-leg. The β-knee, at the junction between I-EGF1 and I-EGF2, is flanked on one side by the PSI domain and on the other by a knob-like projection in the thigh domain.
In the view in FIG. 1A, the lower α-leg is in front of the upper α-leg, whereas the lower β-leg is to the right of the upper β-leg, between it and the α-subunit. In other words, the bent α and β-legs are oriented approximately at right angles rather than parallel to one another. Thus the I-EGF domains of the lower β-leg are deeply buried in a narrow crevice between the upper β-leg on one side and the lower α-leg on the other, with the β I and β-propeller domains helping to form the back of the crevice (FIG. 1A). Exit of the β leg from the crevice appears to be the key step in integrin extension.
Overall extended structure. In the extended conformation of αIIbβ3, the α and β -legs straighten at the knees, and extend away from rather than fold up against the headpiece (FIGS. 1F and G, panel 4). The headpiece fragment excised from the crystal structure cross-correlates excellently with the headpiece seen in EM (FIGS. 1F and G, panels 6-8). Furthermore, cross-correlation demonstrated that in Ca2+ and Mg2+, extended αIIbβ3 predominantly assumes the closed headpiece conformation with low affinity for ligand, as seen in the bent crystal structure, rather than the open conformation with high affinity. Most extended class averages, whether with clasped or unclasped αIIbβ3, show the α-leg crossing over or under the β-leg (FIG. 1F, G, panel 4). Leg crossing appears to be a consequence of upper leg configuration in the bent conformation with the long axis of 1-EGF1 pointing toward the α-knee (FIG. 1A). When the bent crystal structure is extended at the α and β-knees, leg crossing results. However, the legs are highly flexible, and for clarity are shown side-by-side in FIG. 1B. Extended integrins with crossed and uncrossed legs have also been seen for activated αVβ3, αXβ2, and detergent soluble αIIbβ3 integrins (Iwasaki et al., 2005; Nishida et al., 2006; Takagi et al., 2002).
After physiological activation of αIIbβ3 on platelets or treatment with high concentrations of ligands, multiple ligand-induced binding site (LIBS) epitopes are exposed. These epitopes map to the lower β-leg, and to the PSI domain (Honda et al., 1995). The lower β-leg is buried in a cleft in the bent conformation (FIG. 1A), but will be exposed in the extended conformation (FIG. 1B). Similarly, the LIBS epitope in the PSI domain, mapped to residues 1-6 (Honda et al., 1995), is masked by I-EGF2 in the bent conformation (FIG. 1A). By contrast, this epitope is exposed after extension at the I-EGF1/I-EGF2 interface in the β-knee brings I-EGF2 away from the PSI domain (FIG. 1B). The previous functional studies, together with the location of these epitopes within the αIIbβ3 structure, demonstrate that bent and extended αIIbβ3 represent latent and activated integrins, respectively, contradict suggestions that αIIbβ3 is extended in the resting state (Rocco et al., 2008; Ye et al., 2008), and agree with election tomography of active, detergent soluble αIIbβ3 showing that it is extended (Iwasaki et al., 2005).
Methods
Crystallography
Briefly, αIIb and β3 ectodomains were fused to C-terminal segments containing a tobacco etch protease (TEV) site, ACID or BASE coiled-coils, and strep II or His6 (SEQ ID NO: 105) tags, with or without αIIb-L959C and β3-P688C mutations to introduce a disulfide bond. Proteins were purified from CHO Lec 3.2.8.1 cell supernatants. αIIbβ3 with the extra disulfide bond and the C-terminal tag removed by TEV protease in buffer containing 1 mM CaCl2 was crystallized in 10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0. Diffraction data collected at 19-ID of APS was solved using molecular replacement in space group P41. Final refinement with REFMAC5 utilized TLS and NCS. Crystals of the αIIbβ3 ectodomain contain two molecules per asymmetric unit. Density is present for all ectodomain residues (αIIb 1-959 and β3 1-690) except for five loops, and in one molecule, the C-terminal portion of the β-tail domain. Thirteen or 18 N-linked carbohydrate residues are visualized in each molecule. I-EGF1 from the complete αIIb β3 ectodomain was used to model density for this domain in re-refined αIIb β3 headpiece structures with (Springer et al., 2008) or without Fab (Table 1).
Negative stain EM
The clasped and unclasped αIIbβ3 was purified on a Superdex 200 HR column equilibrated with TBS plus 1 mM Ca2+ and 1 mM Mg2+. The peak fraction was adsorbed to glow discharged carbon-coated copper grids, stained with uranyl formate, and inspected with an FEI Tecnai 12 electron microscope operated at 120 kV. Images were acquired at a nominal magnification of 67,000×. Imaging plates were scanned and digitized with a Ditabis micron imaging plate scanner (DITABIS Digital Biomedical Imaging System, AG, Pforzheim, Germany) using a step size of 15 μm and 2×2 pixels were averaged to yield a final pixel size of 4.46 Å at the specimen level. 2,000-5,000 particles were interactively collected, windowed into 75×75-pixel individual images, and subjected to ten cycles of multi-reference alignment and classification. Image processing and cross-correlation using the SPIDER image processing package (Frank et al., 1996) was as described previously (Nishida et al., 2006).
Example 2
Disulfide-Stabilized Integrins for Antibody, Ligand-Binding and Drug Screening
Methods
Production of Soluble αIIbβ3 
DNA constructs of the extracellular domains of soluble αIIbβ3 were made and expressed as described previously (Takagi, et al), or with modifications as described below to introduce an additional disulfide. αIIb extracellular domain residues 1-963 were fused with a tobacco etch virus (TEV) protease site, acidic coiled coil and StrepII tag to give the C-terminal sequence QLLRALEERA/TGGLENLYFQGGENAQCEKELQALEKENAQLEWELQALEKELAQWSHPQFEK (SEQ ID NO: 58), where the slash marks the fusion position, and then inserted into the pcDNA3.1 vector with hygromycin resistance gene. β3 extracellular domain residues 1-690 were fused with a TEV protease site, basic coiled coil and His6 (SEQ ID NO: 105) tag to give the C-terminal sequence VVEEPECPKG/TSGLENLYFQGGKNAQCKKKLQALKKKNAQLKWKLQALKKKLAQGGHHHHH H (SEQ ID NO: 59), where the slash marks the fusion position, and then inserted into the pEF1 vector with the puromycin resistance gene. Cysteine mutations αIIb-L959C and β3-P688C were introduced at the underlined positions in the above sequences using a site-directed mutagenesis kit. Plasmid DNA of the αIIb and β3 constructs was co-transfected into CHO Lec 3.2.8.1 cells using electroporation. Cells were cultured in selection medium containing puromycin and hygromycin for about 10 days until single colonies were obtained. ELISA was used with mAb 7E3 as the capturing antibody and biotinylated mAb AP3 as the detecting antibody to screen for clones with high expression cell lines. Three rounds of screening of approximately 150 colonies yielded one clone (clone #11) with an expression level of about 5 mg/L for the disulfide-bonded construct. The clone was expanded and cultured in roller bottles.
The culture supernatant was concentrated by ultra-filtration and exchanged into 25 mM TrisHCl (pH 8.0) and 300 mM NaCl, plus 5 mM CaCl2 and 10 mM imidazole (loading buffer). The solution was loaded onto a Ni-NTA matrix (QIAGENTM) column (5 ml of resin per 1 liter of culture supernatant) pre-equilibrated with loading buffer. The column was then washed with ten bed-volumes of loading buffer plus 20 mM imidazole and the bound proteins were eluted with five bed-volumes of the loading buffer plus 250 mM imidazole. Eluted proteins were concentrated with an Amicon YM-30 filter (Millipore, Bedford, Mass.) into 20 mM TrisHCl (pH 7.5) and 150 mM NaCl (TBS), plus 5 mM CaCl2, and loaded on a Strep-Tactin column (IBA, St. Louis, Mo.), which was washed with ten bed-volumes of the same buffer. Protein was eluted with the same buffer plus 5 mM desthiobiotin. Purified αIIbβ3 was concentrated with an Amicon YM-30 centrifugal filter to about 1 mg/ml and treated with TEV protease (2.5 units of enzyme per μg αIIbβ3) at 25° C. for 16 hr in TBS plus 5 mM CaCl2. The unclasped αIIbβ3 protein was collected in the flow-through of a second Ni-NTA chromatography step. Purified αIIbβ3 was subjected to Superdex 200 chromatography (Amersham, Piscataway, N.J.) in 20 mM TrisHCl (pH 8), 150 mMNaCl, 1 mM CaCl2.
Negative stain EM.
The clasped and unclasped αIIbβ3 was purified on a Superdex 200 HR column in Tris saline, 1 mM Ca2+, 1 mM Mg2+. The peak fraction was adsorbed to glow discharged carbon-coated copper grids, stained with uranylformate, and inspected with an FEI Tecnai 12 electron microscope operated at 120 kV. Images were acquired at a nominal magnification of 67,000×. Imaging plates were scanned and digitized with a Ditabis micron imaging plate scanner (DITABIS Digital Biomedical Imaging System, AG, Pforzheim, Germany) using a step size of 15 gm and 2×2 pixels were averaged to yield a final pixel size of 4.46 Å at the specimen level. 2,000-5,000 particles were interactively collected, windowed into 75×75-pixel individual images, and subjected to ten cycles of multi-reference alignment and classification. Images were processed and cross-correlated using SPIDER (Frank, et al) as described (Nishida, et al).
Disulfide Crosslinking and Immunoprecipitation
Twenty-four hours after transfection, 293T cells in 12-well plates with 1.5 ml DMEM medium containing 10% FCS were pre-treated with 15 μg/ml of 2-BP for 1 hour, the medium was replaced with 0.75 ml Met, Cys-free RPMI 1640 (Sigma R-7513), supplemented with 10% dialyzed FCS, 10 μl [35S] cysteine/methionine (10mCi/ml, PerkinElmer Life Science), 15 μg/ml 2-BP. After 1.5 h at 37° C., 0.75 ml of RPMI 1640 containing 10% FCS, 500 μg/ml cysteine, 100 μg/ml methionine, and 15 μg/ml 2-BP was added, and cells chased for at least 17 hours. Cells were detached by vigorous pipetting, washed, and suspended (106 cells in 100 μl) in Tris-buffered saline (TBS, 20 mM Tris-HCl, pH 7.5, 150 mM NaCl) containing 1 mM Ca2+/1 mM Mg2+ and proteinase inhibitors (1 μg/ml each aprotinin, leupeptin, and pepstatin). The cells were kept intact or broken by 3 cycles of freezing on dry ice and thawing. Saponin (40 μg/ml) gave results identical to freeze-thawing, but freeze-thawing was adapted as the least membrane-perturbing. After chilling on ice for 5 minutes, 200 μM CuSO4/1000 μM o-phenanthroline was added by 10 fold dilution from stock solution, and cells were incubated on ice for another 10 minutes. N-ethylmaleimide (10 mM) was added and after 10 minutes on ice, cells were lysed with an equal volume of TBS containing 2% Triton X-100 and 0.1% NP-40 for 10 minutes on ice. Cell lysates were cleared by centrifugation at 14,000 RPM for 10 minutes and immunoprecipitated with anti-β3 mAb AP3 and protein G agarose at 4° C. for 1 hour. The precipitated proteins were subjected to non-reducing 7.5% SDS-PAGE. The SDS-PAGE gel was dried and exposed for 3 h to storage phosphor screens which were measured with a Storm PhosphorImager (Molecular Dynamics, Sunnyvale, Calif., United States). Disulfide bond formation was quantitated as the intensity of the disulfide-bonded heterodimer band divided by the sum of the intensity of αIIb, β3, and heterodimer bands. Specific intensity of each band was determined by subtraction of background intensity.
For constitutively cross-linked extracellular and exofacial residues, crosslinking was also measured in redox buffer and after DTT treatment followed by Cu-phenanthroline. For redox buffer treatment, cells were suspended in pH 8.2 TBS containing 1 mM Ca2+/1 mM Mg2+ and 5 mM cysteamine/1 mM cystamine, and incubated at 37° C. for 1 hour. Following addition of 10 mM N-ethylmaleimide, cells were lysed and immunoprecipitated as described above.
Results
Disulfide Bonds Near the Ectodomain-transmembrane Domain Junction of αIIbβ3 
The interface between the αIIb and β3 TM domains has been defined by scanning the TM domains with cysteine and determining the propensity for disulfide bond formation (Luo, et al). Similarly disulfide-bond formation between residues just outside the plasma membrane in intact integrins expressed on the surface of 293 cells was examined (FIG. 2A). A cysteine introduced at residue 688 in the β3 tail domain efficiently formed an inter-subunit disulfide bond with a cysteine introduced at either residue 959 or 960 in the αIIb calf-2 domain (FIG. 2A).
Furthermore, cysteine introduced at β3 686 efficiently disulfide-bonded to cysteine introduced at αIIb 958, 959, and 960, but not 957 (data not shown). Cysteine introduced at residues β3 691 or 693, in the linker between the β3 tail domain and transmembrane domain, also efficiently formed disulfides with residue 965, in the linker between the αIIb calf-2 domain and transmembrane domain (FIG. 2A). αIIb residues 958-960 and β3 residues 686 and 688 are in structured portions of the calf-2 and β-tail domains, respectively. Without wishing to be bound by theory, the ability to form a range of disulfides between these residues indicates that a range of orientations between the calf-2 and β-tail domains can occur on the cell surface. This is consistent with the different orientations seen between calf-2 and β-tail domains in molecules 1 and 2 in αIIbβ3 crystals, even when an αIIb-959 to β3-688 disulfide is present.
Disulfide cross-links between αIIb and β3 transmembrane residues prevent transmission of activation signals across the membrane both in the inside-out and outside-in directions; however, they do not prevent activation of extracellular ligand binding by extracellular signals, such as Mn2+ and activating antibody (Luo, et al; Zhu, et al). Similarly, the α965C/β693C and α965C/β691C mutants with inter-subunit disulfide bonds in the linker regions could be activated by extracellular stimuli to bind the ligand fibrinogen as efficiently as wild-type (FIG. 2B). However, the α959C/β688C and α960C/β688C mutants with inter-subunit disulfide bonds between C-terminal β tail domain and calf-2 residues were partially resistant to activation by Mn2+ and PT25-2 antibody. These results indicate that the tighter association between the α and β subunits enforced by the more ectodomain-proximal disulfide between the β-tail and calf-2 domains makes them more resistant to activation.
The greater stability (higher frequency) of bent particles in αIIbβ3 preparations with than without the αIIb959C/β3688C disulfide correlates with the greater resistance to activation of cell-surface αIIb959C/β3688C than wild-type αIIbβ3 (FIG. 1B). This finding is consistent with conclusions from EM and functional studies on αVβ3 and αXβ2 integrins, that the bent conformation represents the resting state and integrin activation requires extension (Takagi, et al; Nishida, et al).
EM Studies on Disulfide-Mutant Integrins
A similar bent conformation in solution with physiologic divalent cations is seen for three distinct αIIbβ3 constructs in negative stain EM with class averaging. The bent integrins from the three types of constructs are indistinguishable from one another and show excellent cross-correlation with the α11bβ3 crystal structure. One construct was clasped by appending to the α and β ectodomain C-termini 15-residue linkers containing TEV protease sites, followed by an α-helical coiled-coil (Nishida, et al). Association near the C-termini of the α and β subunit ectodomains provided in vivo by association between the αIIb and β3 transmembrane domains (Luo, et al) is mimicked by the clasp (Takagi, et al). The clasped αIIbβ3 particles were 64% bent and 32% extended (with 4% unclassified) (FIG. 1F). Unclasped particles, in which the clasp was removed with TEV protease, were 44% bent and 52% extended. A third construct, which was identical to that used in crystallization, contained cysteines introduced in C-terminal portions of the αIIb and β3 subunits in positions that resulted in efficient disulfide bond formation in cell surface integrins. The disulfide-bonded construct was 100% bent.
The differing proportion of bent particles in the three preparations shows that tighter association near the C-termini correlates with maintenance of the bent conformation, and also, with resistance to activation on the cell surface (FIG. 2). This is in agreement with work on other soluble integrin preparations, and a large body of work on cell surface integrins, which has shown that association of the α and β subunit transmembrane and cytoplasmic domains stabilizes integrins in the low-affinity state and in the bent conformation (reviewed in Luo, et al).
Example 3
αXβ2 was clasped at its C-terminal residues shown herein in the following table. Following the protein sequence, generic coiled coil and hexameric histidine (SEQ ID NO: 105) tag were added to the C terminal of construct. Soluble expression of ectodomain was performed via transfecting 293S cells with PEI (Polyethylenimine) method. Following five days of incubation in 37° C., DMEM media containing 10% FCS and 10% CO2, Western blotting with anti-His antibody was performed to investigate formation disulfide formation. Table below discloses SEQ ID NOS 60-69, respectively, in order of appearance.













PreCission/linkerLG
/coiled coil          /His-tag





          |











Human αX
1079
EKgcg------LQTLFQGP LG AQGEKELQALEKENAQLEWELQALEKELAQ-HHHHHH



 


Human αX
1079
EKYgcg-----LQTLFQGP LG AQGEKELQALEKENAQLEWELQALEKELAQ-HHHHHH


 


Human αX
1079
EKYKgcg----LQTLFQGP LG AQGEKELQALEKENAQLEWELQALEKELAQ-HHHHHH


 


Human αX
1079
EKYKVgcg---LQTLFQGP LG AQGEKELQALEKENAQLEWELQALEKELAQ-HHHHHH


 


Human αX
1079
EKYKVHgcg--LQTLFQGP LG AQGEKELQALEKENAQLEWELQALEKELAQ-HHHHHH


 













PreCission/linkerLG
/coiled coil          /His-tag





           |











Human β2
 672
ECgcg------LQTLFQGP LG AQGKKKLQALKKKNAQLKWKLQALKKKLAQ-HHHHHH



 


Human β2
 672
ECVgcg-----LQTLFQGP LG AQGKKKLQALKKKNAQLKWKLQALKKKLAQ-HHHHHH


 


Human β2
 672
ECVAgcg----LQTLFQGP LG AQGKKKLQALKKKNAQLKWKLQALKKKLAQ-HHHHHH


 


Human β2
 672
ECVAGgcg---LQTLFQGP LG AQGKKKLQALKKKNAQLKWKLQALKKKLAQ-HHHHHH


 


Human β2
 672
ECVAGPgcg--LQTLEQGP LG AQGKKKLQALKKKNAQLKWKLQALKKKLAQ-HHHHHH






5 constructs for both αx and β2 were transfected, and 25 (5×5) combinations of heterodimeric formation were tested by Western blotting. 5 constructs of αx with P677C of β2 constructs resulted in partial formation of disulfide linkage, whereas rest of heterodimeric combinations displayed completely formation dilsulfide. On the other hand, expression level of P677C of β2 construct was comparable to wild type expression based on ELISA, and considerable lessening of expression level was observed for other 20 combinations.







TABLE 1







X-ray diffraction data and refinement









Protein
αIIbβ3 ectodomain
αIIbβ3 headpiece





Spacegroup
P41
P62


Unit cell (a, b, c) (Å)
81.3, 81.3, 654.6
332.1, 332.1, 88.3


(α, β, γ) (°)
90, 90, 90
90, 90, 120


Wavelength (Å)
 0.97934
 0.9760


Resolution (Å)
50-2.55
45-2.90


Number of reflections
614,293/135,066
1,251,268/122,126  


(total/unique)


Completeness (%)
 98.6/93.9*
 98.3/93.9*


I/σ(I)
12.2/2.1*
17.4/3.0*


Rmerge (%)¶
 7.1/56.6*
 9.7/60.2*


Rwork¶¶/Rfree‡‡
0.233/0.268
0.174/0.196










RMSD:
Bond (Å)
0.003
0.006



Angle (°)
0.736
0.659









Ramachandran plot**
95.0%/4.6%/0.4%
96.9%/2.9%/0.2%


PDB code

(prev. 1TYE)





*Asterisked numbers correspond to the last resolution shell.


¶Rmerge = ΣhΣi|Ii(h) − <I(h)>|/ΣhΣiIi(h), where Ii(h) and <I(h)> are the ith and mean measurement of the intensity of reflection h.


¶¶Rwork = Σh||Fobs(h)| − |Fcalc (h)||/Σh|Fobs (h)|, where Fobs (h) and Fcalc (h) are the observed and calculated structure factors, respectively. No I/σ cutoff was applied.


‡‡Rfree is the R value obtained for a test set of reflections consisting of a randomly selected 1.3% subset of the data set excluded from refinement.


**Residues in favorable, allowed, and outlier regions of the Ramachandran plot as reported by MOLPROBITY (Davis et al., 2007).













TABLE 2







Variation in inter-domain angles in integrinsa.














bent αIIbβ3b
bent αIIbβ3c
bent αIIbβ3d
open αIIbβ3e
bent β3f
frag β2g


Domain interface
bent αIIbβ3
bent αVβ3
open αIIbβ3
open αIIbβ3
frag β2
frag β2





α β-propeller-α
0.5°
9.7-9.9°
—
—
—
—


thigh








α thigh-α calf1
1.3°
19-20°
—
—
—
—


α calf1-α calf2
3.4°
14-17°
—
—
—
—


β I-β hybrid
0.2°
6.7-6.7°
 58-70°
1.2-12° 
—
—


β hybrid-β PSI
0.4°
7.2-7.8°
2.0-11°
1.8-9.2°
18-27°
5.0-8.3°


β PSI-β I-EGF1
0.8°
—
3.4-13°
5.7-18° 
5.5-40° 
5.5-41° 


β hybrid-β I-EGF1
0.5°
—
6.8-23°
11-26°
29-51°
3.7-46°


β I-EGF1-β I-EGF2
0.4°
—
—
—
140-170°
67°


β I-EGF2-β I-EGF3
1.2°
—
—
—
8.4-8.5°
—


β I-EGF3-β I-EGF4
2.3°
5.4-7.2°
—
—
—
—


β I-EGF4-β ankle
1.2°
10-11°
—
—
—
—


β I-ankle-β TD
46°h 
18°i
—
—
—
—


α β-propeller-β I
0.2°
3.0-3.3°
 1.7-2.8°
0.6-1.1°
—
—





aEach pair of domains from two molecules were superposed using the first domain, and the change in angle upon superimposing the second domain was calculated. Dashes indicate where no comparison is possible, because only one or no domain pairs are available.


bTwo molecules in current structure (1 × 1).


cTwo molecules in current structure versus PDB code IU8C (2 × 1).


dTwo molecules in current structure versus PDB 2VDR and three molecules in PDB ITYE (2 × 4).


eComparisons among 2VDR and three molecules in ITYE (3 × 4/2).


fTwo molecules in current structure, and PDB 1U8C versus PDB 1YUK, PDB 2P26, and PDB 2P28 (3 × 3 to 3 × 1, depending on fragment length).


gcomparisons among PDB 1YUK, 2P26, and 2P28 (3 to 1 comparisons depending on fragment length).


hResidues common to molecules 1 and 2 in βTD are used, 606-612


iαIIbβ3 molecule 1 compared to αVβ3













TABLE 3





αXβ2-GCG constructs prepared to investigate the clasping of C-terminal region of ectodomain. 


Table discloses SEQ ID NOS 70-81, respectively, in order of appearance.
















Residues changed to Cys are always both preceded and followed by Gly to introduce local flexibility to Cys.


*Clasping sequence of crystallized αXβ2-GCG -TCSH construct are shown on wild type sequence as red and asterisked.
















TABLE 4










Cu-Ph



Constitutive
Redox buffer
oxidation/



disulfideb
treat.
intact call















αIIbβ3


Av-


Av-

Av-
















alpha
beta
Exp1
Ex2
erage
Exp1
Exp2
erage
Exp1
erage



















R957
E686
28

28
0

0




R957
C687
2

2







R957
P688
95
82
88.5







R957
G690
15

15







R957
P691
10

10







R957
D692
12

12







A958
E686
100

100
54

54




A958
C687
2

2







A958
P688
96

96







A958
G690
12

12







A958
P691
15

15







A958
D692
8

8







L959
E686
94

94







L959
C687
2

2







L959
P688
98

98
100

100




L959
G690
30

30







L959
P691
12

12







L959
D692
2

2







E960
E686
92

92
59

59




E960
C687
3

3







E960
P688
91

91
98

98




E960
G690
77

77







E960
P691
64

64







E960
D692
15

15







R962
P691
100

100
56

56
100
100


R962
D692
67

67
5

5
72
72


R962
I693
77

77
3

3
82
82


R962
L694
8

8
0

0
6
6


R962
V695
0

0
0

0
0
0


R962
V696
0

0
0

0
0
0


R962
L697
0

0
0

0
0
0


A963
P691
100

100
30
38
34
100
100


A963
D692
41

41
2
5
3.5
44
44


A963
I693
100

100
19
24
21.5
100
100


A963
L694
5

5
0
0
0
13
13


A963
V695



1
1
1
3
3


A963
V696



0
2
1
13
13


A963
L697



1
0
0.5
6
6


I964
P691
60

60
61
54
57.5
59
59


I964
D692
77

77
21
19
20
80
80


I964
I693
74

74
90
89
89.5
92
92


I964
L694
33

33
5
8
6.5
35
35


I964
V695
18

18
4
6
5
16
16


I964
V696
31

31
30
54
42
39
39


I964
L697
6

6
5
6
5.5
6
6


I964
L698
0

0
0
0
0
0
0





Values are % disulfide bond formation













TABLE 5







052504 FACS (LFA-1 disulfide mutants on 293T cell)









Mean
















Sample No
Sample description
X63
MHM24
m24
A03
KIM127 (1)
KIM127 (2)



















5A
mock
—
—

6.34
6.17
6.27
6.79
5.54



#2
E1061C
G676C

97.38
35.81
59.26
8.27
9.59



#3
K1062C
G676C

117.13
57.43
67.16
11.14
15.81



#4
Q1063C
G676C

95.90
47.81
61.04
12.12
12.15



#5
K1062C
P677C

102.18
43.50
58.30
10.26
9.36



#6
Q1063C
P677C

116.87
52.29
72.99
10.89
14.43



#7
M1064C
P677C

125.86
52.95
77.00
10.77
11.85



#8
Q1063C
N678C

88.46
38.63
52.54
8.54
12.25



#9
M1064C
N678C
4.06
147.12
57.10
88.01
10.03
12.09



WT
WT
WT
5.96
158.96
66.32
105.85
12.15
13.91










Normalization









Mean value normalized with expression level (MHM24)
















Sample No
Sample description
X63
MHM24
m24
A03
KIM127 (1)
KIM127 (2)



















5B
mock
—
—

6.34
—
—
—
—



#2
E1061C
G676C

97.38
0.33
0.58
0.016
0.044



#3
K1062C
G676C

117.13
0.46
0.55
0.039
0.093



#4
Q1063C
G676C

95.90
0.46
0.61
0.060
0.074



#5
K1062C
P677C

102.18
0.39
0.54
0.036
0.040



#6
Q1063C
P677C

116.87
0.42
0.60
0.037
0.080



#7
M1064C
P677C

125.86
0.39
0.59
0.033
0.053



#8
Q1063C
N678C

88.46
0.40
0.56
0.021
0.082



#9
M1064C
N678C
4.06
147.12
0.36
0.58
0.023
0.047



WT
WT
WT
5.96
158.96
0.39
0.65
0.035
0.055










Normalization (WT is set to 1.0)









Relative to wild-type
















Sample No
Sample description
X63
MHM24
m24
A03
KIM127 (1)
KIM127 (2)



















5C
mock
—
—

6.34
—
—
—
—



#2
E1061C
G676C

97.38
0.83
0.89
0.46
0.81



#3
K1062C
G676C

117.13
1.17
0.84
1.12
1.69



#4
Q1063C
G676C

95.90
1.18
0.94
1.69
1.35



#5
K1062C
P677C

102.18
0.99
0.83
1.03
0.73



#6
Q1063C
P677C

116.87
1.06
0.93
1.06
1.47



#7
M1064C
P677C

125.86
0.99
0.91
0.95
0.96



#8
Q1063C
N678C

88.46
1.00
0.86
0.61
1.49



#9
M1064C
N678C
4.06
147.12
0.92
0.89
0.66
0.85



WT
WT
WT
5.96
158.96
1.00
1.00
1.00
1.00










Summary of WB and FACS result









Relative to wild-type
















Sample No
Sample description
disulfide
Expressio
m24
A03
KIM127 (1)
KIM127 (2)



















5D
mock
—
—
−
−
—
—
—
—



#2
E1061C
G676C
++
++
0.83
0.89
0.46
0.81



#3
K1062C
G676C
++
++
1.17
0.84
1.12
1.69



#4
Q1063C
G676C
+
++
1.18
0.94
1.69
1.35



#5
K1062C
P677C
++
++
0.99
0.83
1.03
0.73



#6
Q1063C
P677C
++
+++
1.06
0.93
1.06
1.47



#7
M1064C
P677C
++
+++
0.99
0.91
0.95
0.96



#8
Q1063C
N678C

++
1.00
0.86
0.61
1.49



#9
M1064C
N678C
+
+++
0.92
0.89
0.66
0.85



WT
WT
WT
−
+++
1.00
1.00
1.00
1.00










Summary of RB result









ve to wild-type












Sample No
Sample description
disulfide
Expression

















5E
mock
—
—
−
−




#2
E1061C
G676C
++
++




#3
K1062C
G676C
++
++

## Claims

1. An integrin polypeptide composition comprising a modified integrin polypeptide locked in a closed conformation comprising one extracellular alpha and one extracellular beta subunit wherein the alpha subunit comprises human integrin αIIb N terminal extracellular domain L959C mutant set forth in SEQ ID NO:48 or human integrin αIIb N terminal extracellular domain E960C mutant set forth in SEQ ID NO: 49, and wherein the beta subunit comprises human integrin β3 N terminal extracellular domain V664C mutant set forth in SEQ ID NO: 52 or human integrin β3 N terminal extracellular domain P688C mutant set forth in SEQ ID NO: 53.

2. The integrin polypeptide of claim 1, wherein the human integrin is human platelet integrin.

3. An integrin polypeptide composition comprising a modified integrin polypeptide locked in a closed conformation comprising a modified αIIb comprising SEQ ID NO: 48 and a modified β3 comprising SEQ ID NO: 53.