US20040229287A1 - Method of preparing a protein array based on biochemical protein-protein interaction - Google Patents

Method of preparing a protein array based on biochemical protein-protein interaction Download PDF

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US20040229287A1
US20040229287A1 US10/820,403 US82040304A US2004229287A1 US 20040229287 A1 US20040229287 A1 US 20040229287A1 US 82040304 A US82040304 A US 82040304A US 2004229287 A1 US2004229287 A1 US 2004229287A1
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Taka-Aki Sato
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Columbia University in the City of New York
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54353—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals with ligand attached to the carrier via a chemical coupling agent
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4747—Apoptosis related proteins

Definitions

  • Fas (APO-1/CD95) and its ligand have been identified as important signal-mediators of apoptosis (Itoh, et al. 1991)
  • the structural organization of Fas (APO-1/CD95) has suggested that it is a member of the tumor necrosis factor receptor superfamily, which also includes the p75 nerve growth factor receptor (NGFR) (Johnson, et al. 1986), the T-cell-activation marker CD27 (Camerini, et al. 1991), the Hodgkin-lymphoma-associated antigen CD30 (Smith, et al. (1993), the human B cell antigen CD40 (Stamenkovic, et al.
  • Fas-interacting signal transducing molecules such as Fas-associated phosphatase-1 (FAP-1)(FIG. 1) (Sato, et al. 1995), FADD/MORT1 (Chinnaiyan, et al. 1995; Boldin, et al. 1995; Kischkel, et al. 1995) and RIP (Stanger, et al. 1995), have been identified using yeast two-hybrid and biochemical approaches. All but FAP-1 associate with the functional cell death domain of Fas and overexpression of FADD/MORT1 or RIP induces apoptosis in cells transfected with these proteins. In contrast, FAP-1 is the only protein that associates with the negative regulatory domain (C-terminal 15 amino acids) (Ito, et al. 1993) of Fas and that inhibits Fas-induced apoptosis.
  • FAP-1 Fas-associated phosphatase-1
  • FAP-1 has several alternatively-spliced forms that are identical to PTP-BAS/hPTP1E/PTPL1, (Maekawa, et al. 1994; Banville, et al. 1994; Saras, et al. 1994) and contains a membrane-binding region similar to those found in the cytoskeleton-associated proteins, ezrin, (Gould et al. 1989) radixin (Funayama et al. 1991) moesin (Lankes, et al. 1991), neurofibromatosis type II gene product (NFII) (Rouleau, et al. 1993), and protein 4.1 (Conboy, et al.
  • FAP-1 interestingly contains six GLGF (PDZ/DHR) repeats that are thought to mediate intra-and inter-molecular interactions among protein domains.
  • the third GLGF repeat of FAP-1 was first identified as a domain showing the specific interaction with the C-terminus of Fas receptor (Sato, et al. 1995). This suggests that the GLGF domain may play an important role in targeting proteins to the submembranous cytoskeleton and/or in regulating biochemical activity.
  • GLGF repeats have been previously found in guanylate kinases, as well as in the rat post-synaptic density protein.
  • PSD-95 Cho, et al. 1992
  • dlg-1 lethal-(1)-disc-large-1 [dlg-1]
  • These repeats may mediate homo- and hetero-dimerization, which could potentially influence PTPase activity, binding to Fas, and/or interactions of FAP-1 with other signal transduction proteins.
  • This disclosure provides a method of preparing a protein array based on biochemical protein-protein interaction, comprising (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain, and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the first protein array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • This disclosure also provides a method of preparing a protein array, (a) depositing on a substrate an array of first proteins, each first protein comprising a corresponding PDZ domain, and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the array of first proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein, for each of the first proteins, binding to the PDZ domain of the first protein, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • This disclosure also provides a method of preparing a protein array, (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain, and (b) applying a plurality of second proteins, each of which comprises a corresponding amino acid sequence (S/T)-X-(V/I/L)-COOH, to corresponding elements of the first protein array, for each of the second proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein in the corresponding array element, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • This disclosure also provides a method of preparing a protein array, comprising (a) depositing on a substrate an array of a first polypeptide, the first polypeptide comprising a PDZ domain, and (b) applying a second polypeptide which-comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH to the first polypeptide array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second polypeptide binding to the PDZ domain of the first polypeptide, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • FIG. 1 Diagram of Fas-associated phosphatase-1 protein, showing the six GLGF (PDZ/DHR) domain repeats; comparison of similar membrane binding sites with other proteins and proteins that contain GLGF (PDZ/DHR), repeats.
  • FIGS. 2A, 2B, 2 C and 2 D Mapping of the minimal region of the C-terminal of Fas required for the binding to FAP-1. Numbers at right show each independent clone. (FIGS. 2C and 2D).
  • FIGS. 3A, 3B and 3 C Inhibition assay of Fas/FAP-1 binding in vitro.
  • FIGS. 4A, 4B, 4 C and 4 D are identical to FIGS. 4A, 4B, 4 C and 4 D.
  • FIGS. 5A, 5B, 5 C, 5 D, 5 E and 5 F Microinjection of Ac-SLV into the DLD-1 cell line. Triangles identify the cells both that were could be microinjected with Ac-SLV and that showed condensed chromatin identified. On the other hand, only one cell of the area appeared apoptotic when microinjected with Ac-SLY.
  • FIG. 6 Quantitation of apoptosis in microinjected DLD-1 cells.
  • FIG. 8 Representation of the structural characteristics of p75 NGFR (low-affinity nerve growth factor receptor).
  • FIG. 9 Comparison of the C-terminal ends of Fas and p75 NGFR.
  • FIG. 10 In vitro interaction of 35 S-labeled FAP-1 with various receptors expressed as GST fusion proteins.
  • the indicated GST fusion proteins immobilized on glutathione-Sepharose beads were incubated with in vitro translated, 35 S-labeled FAP-1 protein. After the beads were washed, retained FAP-1 protein was analyzed by, SDS-PAGE and autoradiography.
  • FIGS. 11A and 11B In vitro interaction 35 S-labeled FAP-1 with GST-p75 deletion mutants.
  • FIG. 11 A Schematic representation of the GST fusion proteins containing the cytoplasmic domains of p75 and p75 deletion mutants. Binding of FAP-1 to the GST fusion proteins with various p75 deletion mutants is depicted at the right and is based on data from ( 2 B).
  • FIG. 12 The association between LexA-C-terminal cytoplasmic region of p75NGFR and VP16-FAP-1. The indicated yeast strains were constructed by transformation and the growth of colonies was tested. +/ ⁇ indicates the growth of colonies on his plate.
  • FIGS. 13A-13C provide schematic representations of a method of preparing a protein array based on biochemical protein-protein interaction, according to an embodiment of the present disclosure.
  • FIGS. 14A-14C provide schematic representations of some exemplary types of substrates that may be used for preparing a protein array based on biochemical protein-protein interaction.
  • amino acid residues are abbreviated as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
  • the present disclosure provides a method of preparing a protein array based on biochemical protein-protein interaction, comprising the steps of: (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain; and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the first protein array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein.
  • a second protein which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH
  • Each hyphen represents a peptide bond
  • each parenthesis encloses amino acids which are alternatives to one other
  • each slash within such parentheses separates the alternative amino acids
  • the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • amino acid sequence (S/T)-X-(V/I/L) may be fused to the C-terminal of the second protein.
  • the protein array may be maintained under physiological condition, and used to screen one or more drug targets.
  • the first protein deposited in step (a) may be in a soluble buffer or immobilized in a gel.
  • the substrate may include a plurality of microwells contained therein, and the first protein is deposited in step (a) into the microwells.
  • the substrate may include a glass plate, and the first protein array is printed onto the glass plate in step (a).
  • the substrate may include a glass plate and a plurality of gel pads on the glass plate, and the first protein is deposited in step (a) onto the gel pads.
  • the substrate comprises one or more filter membranes.
  • the first protein may be deposited-on the substrate by a robot.
  • the array may include an oligonucleotide, a sugar, messenger RNA and/or DNA.
  • the arrays prepared with the methodologies provided by this disclosure may include, but are not limited to, antibodies, inorganic compounds, organic compounds, peptides, peptidomimetic compounds, polypeptides or proteins, fragments or derivatives which share some or all properties, e.g. fusion proteins.
  • the components of the arrays may be naturally occurring and obtained by purification, or may be non-naturally occurring and obtained by synthesis. Proteins, enzymes, antibodies, compositions, etc., may be obtained, when available, from commercial sources, such as Sigma (U.S.A.).
  • the first protein array which is deposited on the substrate need not be a single protein, but rather may be a plurality of different proteins having one or more PDZ domains.
  • the second protein which is applied to the protein array need not be a single protein, but rather may be a plurality of different proteins which comprise one or more amino acid sequences (S/T)-X-(V/I/L)-COOH.
  • the present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of first proteins, each first protein comprising a corresponding PDZ domain; and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the array of first proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein, for each of the first proteins, binding to the PDZ domain of the first protein.
  • a second protein which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH
  • Each hyphen represents a peptide bond
  • each parenthesis encloses amino acids which are alternatives to one other
  • each slash within such parentheses separates the alternative amino acids
  • the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • the present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain; and (b) applying a plurality of second proteins, each of which comprises a corresponding amino acid sequence (S/T)-X-(V/I/L)-COOH, to corresponding elements of the first protein array, for each of the second proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein in the corresponding array element.
  • Each hyphen represents a peptide bond
  • each parenthesis encloses amino acids which are alternatives to one other
  • each slash within such parentheses separates the alternative amino acids
  • the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • the present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of a first polypeptide, the first polypeptide comprising a PDZ domain; and (b) applying a second polypeptide which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH to the first polypeptide array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second polypeptide binding to the PDZ domain of the first polypeptide.
  • each hyphen represents a peptide bond
  • each parenthesis encloses amino acids which are alternatives to one other
  • each slash within such parentheses separates the alternative amino acids
  • the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids.
  • the array may include an oligonucleotide, a sugar, messenger RNA and/or DNA.
  • FIGS. 13A-13C and 14 A- 14 C Some embodiments of protein array preparation are described exemplarily below, with reference to FIGS. 13A-13C and 14 A- 14 C, to illustrate some methodologies contemplated by the subject disclosure.
  • One skilled in the art would recognize that these methodologies (and other aspects of the disclosure described herein) may be adapted for preparing arrays that include one or more other polypeptides, oligonucleotides, sugars, messenger RNAs, DNAs, and/or other compounds.
  • the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein. (A) binds to the PDZ domain of, the first protein (P) [FIG. 13C].
  • the protein array may be used to screen drugs X, Y, Z, etc.
  • a substrate comprising a glass plate and a plurality of microwells (FIG. 14C) formed by, for example, an enclosing hydrophobic Teflon mask may be used (see, for example, Mendoza, et al. 1999).
  • the protein having a PDZ domain is dissolved in a buffered solution.
  • the protein solution is then printed as an array on the substrate through, for example, a capillary-based print head attached to a X-Y-Z robot (or another type of microdispensing liquid handling robot system).
  • the protein may also be printed onto a treated glass slide without wells (FIG. 14A).
  • a treated glass slide without wells (FIG. 14A).
  • use of such a substrate has the disadvantage of having higher evaporation and a greater risk of cross contamination.
  • gels may be used to immobilize the protein having a PDZ domain. Preparation of protein microchips using gel pads is described by, for example, Arenkov, et al. 2000.
  • the gel pads are deposited as a micromatrix on a glass slide (FIG. 14B) and then treated according to the composition of the gel pads (for example, photopolymerization may be used for polyacrylamide gel pads).
  • the protein which may be dissolved in a (for example, phosphate) buffered solution, is then transferred onto the gel pads, for example, via a pin by using a robot or a manual device.
  • the pin and micromatrix are kept at dew point to avoid evaporation of the protein solution.
  • the protein is chemically attached to the gels.
  • any of a number of methodologies may be used.
  • An advantage of using gel support for fixation of biological compounds is its large capacity for immobilized compounds.
  • the gel pads in the array are separated from each other by a hydrophobic surface. Therefore, gel pad arrays can be used as micro-test tubes to carry out specific interactions and chemical and enzymatic procedures with microchip substances.
  • Filter membranes also may be used to immobilize the protein.
  • An appropriately selected membrane passively binds to, and thereby immobilizes, the protein, to produce protein filters.
  • the protein solution may be labeled by covalent linkage of a fluorecent dye to the amino groups on the protein.
  • Fluorescence microscopy methodologies may be in conjunction with the protein-protein interaction (described exemplarily below), for example, to screen drug targets.
  • a second protein which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH is applied to the micromatrix.
  • the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binds to the PDZ domain of the first protein.
  • a wash may be applied.
  • the first protein which is deposited as an array on the substrate may comprise the amino acid sequence (S/T)-X-(V/I/L)-COOH, and the second protein which is applied to the first protein array may comprise the PDZ domain.
  • PCR mutagenesis with degenerate oligonucleotides was employed according to a protocol described elsewhere (Hill, et al.: 1987). Based on the homology-between human and rat, two palindromic sequences were designed for construction of semi-random library. The two primers used were 5′-CGGAATTCNNNNNNNNNAACAGCNNNNNNNNNAATGAANNNCAAAGTCTGNNNT GAGGATCCTCA-3′ (Seq. I.D. No. 31) and 5′-CGGAATTCGACTCAGAA NNNNNNAACTTCAGANNNNNNATCNNNNNNNNNGTCTGAGGATCCTCA-3′ (Seq. I.D. No.
  • the two primers (each 200 pmol), purified by HPLC, were annealed at 70° C. for 5 minutes and cooled at 23° C. for 60 minutes.
  • a klenow fragment (5 U) was used for filling in with a dNTP mix (final concentration, 1, mM per each dNTP) at 23° C. for 60 minutes.
  • the reaction was stopped with 1 ⁇ l of 0.5 M EDTA and the DNA was purified with ethanol precipitation.
  • the resulting double-stranded DNA was digested with EcoRI and BamHI and re-purified by electrophoresis on non-denaturing polyacrylamide gels.
  • the double-strand oligonucleotides were then ligated into the EcoRI-BamHI sites of the pBTM116 plasmid.
  • the ligation mixtures were electroporated into the E. coli XL1-Blue MRF′ (Stratagene) for the plasmid library.
  • the large scale transformation was carried out as previously reported.
  • the plasmid library was transformed into L40-strain cells (MATa, trp1, leu2, his3, ade2, LYS2: (lexAop) 4 -HIS3, URA3:: (lexAop) 8 -lacZ) carrying the plasmid pVP16-31 containing a FAP-1 cDNA (Sato, et al.
  • Clones that formed on histidine-deficient medium were transferred to plates containing 40 ⁇ g/ml X-gal to test for a blue reaction product ( ⁇ -gal + ) in plate and filter assays.
  • the clones selected by His + and ⁇ -gal + assay were tested for further analysis.
  • the palindromic oligonucleotide, 5′-CGGAATTC-(NNN) 4-1 -TGAGGATCCTCA-3′ (Seq. I.D. No. 33), was used for the construction of the random peptide library.
  • HFAP-10 cDNA (Sato, et al. 19-95) subcloned into the Bluescript vector pSK-II (Stratagene) was in vitro-translated from an internal methionine codon in the presence of 35 S-L-methionine using a coupled in vitro transcription/translation system (Promega, TNT lysate) and T7 RNA polymerase.
  • the resulting 35 S-labeled protein was incubated with GST-Fas fusion proteins that, had been immobilized on GST-Sepharose 4B affinity beads (Pharmacia) in a buffer containing 150 mM NaCl, 50 mM Tris [pH 8.0], 5 mM DTT, 2 mM EDTA, 0.1% NP-40, 1 mM PMSF, 50 ⁇ g/ml leupeptin, 1 mM Benzamidine, and 7 ⁇ g/ml pepstatin for 16 hours at 4° C. After washing vigorously 4 times in the same buffer, associated proteins were recovered with the glutathione-Sepharose beads by centrifugation, eluted into boiling Laemmli buffer, and analyzed by SDS-PAGE and fluorography.
  • the bait plasmids pBTM116 (LexA)-SLV, -PLV, -SLY, and -SLA, were constructed and transformed into L40-strain with pVP16-FAP-1 or -ras. Six independent clones from each transformants were picked up for the analysis of growth on histidine-deficient medium. GST-Fas, -SLV, and PLV were purified with GST-Sepharose 4B affinity beads (Pharmacia). The methods for in vitro binding are described above.
  • DLD-1 human colon cancer cells were cultured in RPMI 1640 medium containing 10% FCS.
  • cells were plated on CELLocate (Eppendorf) at 1 ⁇ 10 5 cells/2 ml in a 35 mm plastic culture dish and grown for 1 day.
  • Fas monoclonal antibodies CH11 (MBL International) was added at the concentration of 500 ng/ml. All microinjection experiments were performed using an automatic microinjection system (Eppendorf transjector 5246, micro-manipulator 5171 and Femtotips) (Pantel, et al. 1995). Synthetic tripeptides were suspended in 0.1%.
  • FITC-Dextran (Sigma)/K-PBS at the concentration of 100 mM.
  • the samples were microinjected into the cytoplasmic region of DLD-1 cells. Sixteen to 20 hours postinjection, the cells were washed with PBS and stained with 10 ⁇ g/ml Hoechst 33342 in PBS. After incubation at 37° C. for 30 minutes, the cells were photographed and the cells showing condensed chromatin were counted as apoptotic.
  • FIG. 2A In order to identify the minimal peptide stretch in the C-terminal region of the Fas receptor necessary for FAP-1 binding, an in vitro inhibition assay of Fas/FAP-1 binding was used using a series of synthetic peptides as well as yeast two-hybrid system peptide libraries (FIG. 2A) First, semi-random libraries (based on the homology between human and rat Fas) (FIGS. 2B and 2C) of 15 amino acids fused to a LexA DNA binding domain were constructed and co-transformed into yeast strain L40 with pVP16-31 (Sato, et al. 1995) that was originally isolated as FAP-1.
  • FAP-1 was originally identified as a membrane-associated protein tyrosine phosphatase which binds to the C-terminus of Fas, and possesses six PDZ domains (also known as DHR domain or GLGF repeat). PDZ domain has recently-been shown as a novel module for specific protein-protein interaction, and it appears to be important in the assembly of membrane proteins and also in linking signaling molecules in a multiprotein complex. In recent comprehensive studies, it was found that the third PDZ domain of FAP-1 specifically recognized the sequence motif t(S/T)-X-V and interacts with the C-terminal three amino acids SLV of Fas (FIG. 9).

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Abstract

A method of preparing a protein array based on biochemical protein-protein interaction is provided. An array of a first protein which comprises a PDZ domain is deposited on a substrate. A second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH (each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids), is applied to the first protein array. The amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein is bound to the PDZ domain of the first protein.

Description

  • [0001] The subject matter disclosed herein was made with Government support under Grant No. R01GM55147-01 from the National Institutes of Health of the United States Department of Health and Human Services. Accordingly, the U.S. Government may have certain rights in this application.
    • BACKGROUND
  • Throughout this application, various publications are referenced by author and date. Full citations for these publications may be found listed alphabetically at the end of the specification immediately preceding Sequence Listing and the claims. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as known to those skilled therein as of the date of the invention described and claimed herein. [0002]
  • Fas (APO-1/CD95) and its ligand have been identified as important signal-mediators of apoptosis (Itoh, et al. 1991) The structural organization of Fas (APO-1/CD95) has suggested that it is a member of the tumor necrosis factor receptor superfamily, which also includes the p75 nerve growth factor receptor (NGFR) (Johnson, et al. 1986), the T-cell-activation marker CD27 (Camerini, et al. 1991), the Hodgkin-lymphoma-associated antigen CD30 (Smith, et al. (1993), the human B cell antigen CD40 (Stamenkovic, et al. 1989), and T cell antigen OX40 (Mallett, et al. 1990). Genetic mutations of both Fas and its ligand have been associated with lymphoproliferative and autoimmune disorders in mice (Watanabe-Fukunaga, et al. 1992; Takahashi, et al. 1994). Furthermore, alterations of Fas expression level have been thought to lead to the induction of apoptosis in T-cells infected with human immunodeficiency virus (HIV) (Westendorp, et al. 1995). [0003]
  • Several Fas-interacting signal transducing molecules, such as Fas-associated phosphatase-1 (FAP-1)(FIG. 1) (Sato, et al. 1995), FADD/MORT1 (Chinnaiyan, et al. 1995; Boldin, et al. 1995; Kischkel, et al. 1995) and RIP (Stanger, et al. 1995), have been identified using yeast two-hybrid and biochemical approaches. All but FAP-1 associate with the functional cell death domain of Fas and overexpression of FADD/MORT1 or RIP induces apoptosis in cells transfected with these proteins. In contrast, FAP-1 is the only protein that associates with the negative regulatory domain (C-[0004] terminal 15 amino acids) (Ito, et al. 1993) of Fas and that inhibits Fas-induced apoptosis.
  • FAP-1 (PTPN13) has several alternatively-spliced forms that are identical to PTP-BAS/hPTP1E/PTPL1, (Maekawa, et al. 1994; Banville, et al. 1994; Saras, et al. 1994) and contains a membrane-binding region similar to those found in the cytoskeleton-associated proteins, ezrin, (Gould et al. 1989) radixin (Funayama et al. 1991) moesin (Lankes, et al. 1991), neurofibromatosis type II gene product (NFII) (Rouleau, et al. 1993), and protein 4.1 (Conboy, et al. 1991), as well as in the PTPases PTPH1 (Yang, et al. 1991), PTP-MEG (Gu, et al. 1991), and PTPD1 (Vogel, et al. 1993). FAP-1 intriguingly contains six GLGF (PDZ/DHR) repeats that are thought to mediate intra-and inter-molecular interactions among protein domains. The third GLGF repeat of FAP-1 was first identified as a domain showing the specific interaction with the C-terminus of Fas receptor (Sato, et al. 1995). This suggests that the GLGF domain may play an important role in targeting proteins to the submembranous cytoskeleton and/or in regulating biochemical activity. GLGF repeats have been previously found in guanylate kinases, as well as in the rat post-synaptic density protein. (PSD-95) (Cho, et al. 1992), which is a homolog of the [0005] Drosophila tumor suppressor protein, lethal-(1)-disc-large-1 [dlg-1] (Woods, et al 1991; Kitamura, et al. 1994). These repeats may mediate homo- and hetero-dimerization, which could potentially influence PTPase activity, binding to Fas, and/or interactions of FAP-1 with other signal transduction proteins. Recently, it has also been reported that the different PDZ domains of proteins interact with the C-terminus of ion channels and other proteins (FIG. 1) (TABLE 1) (Kornau, et al. 1995; Kim, et al. 1995; Matsumine, et al. 1996).
    TABLE 1
    Proteins that interact with PDZ domains.
    C-terminal Associated
    Protein sequence protein Reference
    Fas (APO-1/CD95) SLV FAP-1 2
    NMDA receptor SDV PSD95 3
    MR2 subunit
    Shaker-type K+ TDV PSD95 & DLG 4
    channel
    APC TEV DLG 5
  • A recent trend in biology, biotechnology and medicine is the use of arrays of immobilized biological compounds in studies of immunoassays and enzymatic reactions (see Mendoza, et al. 1999; Arenkov, et al. 2000). For example, mass-sensing, multianalyte microarray immunoassays have been performed (Rowe, et al. 1998; Silzel, et al. 1998). The use of arrays allows for large scale and high-throughput studies of multiple samples in parallel. Integration of microarray technology into the experimental methodology also may increase efficiency in many instances, such as through reducing the volume of samples and reagents required. [0006]
  • It would be desirable to have high-throughput and low cost methodologies for preparing protein arrays based on protein-protein interaction, and which keep the proteins in a functionally active state and allow, for example, multiple drug screenings under physiological conditions. [0007]
    • SUMMARY OF THE INVENTION
  • This disclosure provides a method of preparing a protein array based on biochemical protein-protein interaction, comprising (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain, and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the first protein array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0008]
  • This disclosure also provides a method of preparing a protein array, (a) depositing on a substrate an array of first proteins, each first protein comprising a corresponding PDZ domain, and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the array of first proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein, for each of the first proteins, binding to the PDZ domain of the first protein, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0009]
  • This disclosure also provides a method of preparing a protein array, (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain, and (b) applying a plurality of second proteins, each of which comprises a corresponding amino acid sequence (S/T)-X-(V/I/L)-COOH, to corresponding elements of the first protein array, for each of the second proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein in the corresponding array element, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0010]
  • This disclosure also provides a method of preparing a protein array, comprising (a) depositing on a substrate an array of a first polypeptide, the first polypeptide comprising a PDZ domain, and (b) applying a second polypeptide which-comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH to the first polypeptide array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second polypeptide binding to the PDZ domain of the first polypeptide, wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0011]
    • BRIEF DESCRIPTION OF THE FIGURES
  • FIG. 1. Diagram of Fas-associated phosphatase-1 protein, showing the six GLGF (PDZ/DHR) domain repeats; comparison of similar membrane binding sites with other proteins and proteins that contain GLGF (PDZ/DHR), repeats. [0012]
  • FIGS. 2A, 2B, [0013] 2C and 2D. Mapping of the minimal region of the C-terminal of Fas required for the binding to FAP-1. Numbers at right show each independent clone. (FIGS. 2C and 2D).
  • [0014] 2A. Strategy for screening of a random peptide library by the yeast two-hybrid system.
  • [0015] 2B. Alignment of the C-terminal 15 amino acids of Fas between human (Sequence I.D. No. 5), rat (Sequence I.D. No. 6), and mouse (Sequence I.D. No. 7).
  • [0016] 2C. The results of screening a semi-random peptide library. Top row indicates the amino acids which were fixed based on the homology between human and rat. Dash lines show unchanged amino acids.
  • [0017] 2D. The results of screening a random peptide library (Sequence I.D. No. 8, Sequence I.D. No. 9, Sequence I.D. No. 10, Sequence I.D. No. 11, Sequence I.D. No. 12, Sequence I.D. No. 13, Sequence I.D. No. 14, Sequence I.D. No. 15, Sequence I.D. No. 16, Sequence I.D. No. 17, respectively).
  • FIGS. 3A, 3B and [0018] 3C. Inhibition assay of Fas/FAP-1 binding in vitro.
  • [0019] 3A. Inhibition assay of Fas/FAP-1 binding using the C-terminal 15 amino acids of Fas. GST-Fas fusion protein (191-355) was used for in vitro binding assay (lane 1, 3-10). GST-Fas fusion protein (191-320) (lane 2) and 1 mM human PAMP (N-terminal 20 amino acids of proadrenomedullin, M.W. 2460.9) (lane 3) were used as negative controls. The concentrations of the C-terminal 15 amino acids added were 1 (lane 4), 3 (lane 5), 10 (lane 6), 30 (lane 7), 100 (lane 8), 300 (lane 9), and 1000 μM (lane 10).
  • [0020] 3B. Inhibition assay of Fas/FAP-1 binding using the truncated peptides corresponding to the C-terminal 15 amino acids of Fas. All synthetic peptides were acetylated for this inhibition assay (Sequence I.D. No. 4, Sequence I.D. No. 18, Sequence I.D. No. 19, Sequence I.D. No. 20, Sequence I.D. No. 21, Sequence I.D. No. 22, Sequence I.D. No. 23, respectively).
  • [0021] 3C. Inhibitory effect of Fas/FAP-1 binding using the scanned tripeptides.
  • FIGS. 4A, 4B, [0022] 4C and 4D.
  • [0023] 4A. Interaction of the C-terminal 3 amino acids of Fas with FAP-1 in yeast.
  • [0024] 4B. Interaction of the C-terminal 3 amino acids of Fas with FAP-1 in vitro.
  • [0025] 4C. Immuno-precipitation of native Fas with GST-FAP-1.
  • [0026] 4D. Inhibition of Fas/FAP-1 binding with Ac-SLV or Ac-SLY.
  • FIGS. 5A, 5B, [0027] 5C, 5D, 5E and 5F. Microinjection of Ac-SLV into the DLD-1 cell line. Triangles identify the cells both that were could be microinjected with Ac-SLV and that showed condensed chromatin identified. On the other hand, only one cell of the area appeared apoptotic when microinjected with Ac-SLY.
  • [0028] 5A. Representative examples of the cells microinjected with Ac-SLV in the presence of 500 ng/ml CH11 are shown in phase contrast.
  • [0029] 5B. Representative examples of the cells microinjected with AC-SLY in the presence of 500 ng/ml CH11 are shown in phase contrast.
  • [0030] 5C. Representative examples of the cells microinjected with Ac-SLV in the presence of 500 ng/ml CH11 are shown stained with FITC.
  • [0031] 5D. Representative examples of the cells microinjected with AC-SLY in the presence of 500 ng/ml CH11 are shown stained with FITC.
  • [0032] 5E. Representative examples of the cells miicroinjected with Ac-SLV in the presence of 500 ng/ml CH11 are shown with fluorescent DNA staining with Hoechst 33342.
  • [0033] 5F. Representative examples of the cells microinjected with AC-SLY in the presence of 500 ng/ml CH11 are shown in fluorescent DNA staining with Hoechst 33342.
  • FIG. 6. Quantitation of apoptosis in microinjected DLD-1 cells. [0034]
  • FIGS. 7A, 7B, [0035] 7C, 7D, 7E, 7F, 7G, and 7H.
  • [0036] 7A. Amino acid sequence of human nerve growth factor receptor (Sequence I.D. No. 24).
  • [0037] 7B. Amino acid sequence of human CD4 receptor (Sequence I.D. No. 25).
  • [0038] 7C. The interaction of Fas-associated phosphatase-1 to the C-terminal of nerve growth factor receptor (NGFR)(p75).
  • [0039] 7D. Amino acid sequence of human colorectal mutant cancer protein (Sequence I.D. No. 26).
  • [0040] 7E. Amino acid sequence of protein kinase C, alpha type (Sequence I.D. No. 27).
  • [0041] 7F. Amino acid sequence of serotonin 2A receptor (Sequence I.D. No. 28).
  • [0042] 7G. Amino acid sequence of serotonin 2B receptor (Sequence I.D. No. 29).
  • [0043] 7H. Amino acid sequence of adenomatosis polyposis coli protein (Sequence I.D. No. 30).
  • FIG. 8. Representation of the structural characteristics of p75 NGFR (low-affinity nerve growth factor receptor). [0044]
  • FIG. 9. Comparison of the C-terminal ends of Fas and p75 NGFR. [0045]
  • FIG. 10. In vitro interaction of [0046] 35S-labeled FAP-1 with various receptors expressed as GST fusion proteins. The indicated GST fusion proteins immobilized on glutathione-Sepharose beads were incubated with in vitro translated, 35S-labeled FAP-1 protein. After the beads were washed, retained FAP-1 protein was analyzed by, SDS-PAGE and autoradiography.
  • FIGS. 11A and 11B. In vitro interaction [0047] 35S-labeled FAP-1 with GST-p75 deletion mutants.
  • [0048] 11A. Schematic representation of the GST fusion proteins containing the cytoplasmic domains of p75 and p75 deletion mutants. Binding of FAP-1 to the GST fusion proteins with various p75 deletion mutants is depicted at the right and is based on data from (2B).
  • [0049] 11B. Interaction of in vitro translated, 35S-labeled FAP-1 protein with various GST fusion proteins immobilized on glutathione-Sepharose beads.
  • After the beads were washed, retained FAP-1 protein was analyzed by SDS-PAGE and autoradiography. [0050]
  • FIG. 12. The association between LexA-C-terminal cytoplasmic region of p75NGFR and VP16-FAP-1. The indicated yeast strains were constructed by transformation and the growth of colonies was tested. +/− indicates the growth of colonies on his plate. [0051]
  • FIGS. 13A-13C provide schematic representations of a method of preparing a protein array based on biochemical protein-protein interaction, according to an embodiment of the present disclosure. [0052]
  • FIGS. 14A-14C provide schematic representations of some exemplary types of substrates that may be used for preparing a protein array based on biochemical protein-protein interaction.[0053]
    • DETAILED DESCRIPTION
  • As used herein, amino acid residues are abbreviated as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr. [0054]
  • In order to facilitate an understanding of the material which follows, one may refer to Sambrook, et al., 1989 for certain frequently occurring methods and/or terms which are described therein. [0055]
  • The present disclosure provides a method of preparing a protein array based on biochemical protein-protein interaction, comprising the steps of: (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain; and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the first protein array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein. Each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0056]
  • The amino acid sequence (S/T)-X-(V/I/L) may be fused to the C-terminal of the second protein. [0057]
  • The protein array may be maintained under physiological condition, and used to screen one or more drug targets. [0058]
  • Further, the first protein deposited in step (a) may be in a soluble buffer or immobilized in a gel. [0059]
  • Further, the substrate may include a plurality of microwells contained therein, and the first protein is deposited in step (a) into the microwells. In another embodiment, the substrate may include a glass plate, and the first protein array is printed onto the glass plate in step (a). According to another embodiment, the substrate may include a glass plate and a plurality of gel pads on the glass plate, and the first protein is deposited in step (a) onto the gel pads. In yet another embodiment, the substrate comprises one or more filter membranes. In any event, the first protein may be deposited-on the substrate by a robot. [0060]
  • Further, the array may include an oligonucleotide, a sugar, messenger RNA and/or DNA. [0061]
  • In addition, the arrays prepared with the methodologies provided by this disclosure may include, but are not limited to, antibodies, inorganic compounds, organic compounds, peptides, peptidomimetic compounds, polypeptides or proteins, fragments or derivatives which share some or all properties, e.g. fusion proteins. The components of the arrays may be naturally occurring and obtained by purification, or may be non-naturally occurring and obtained by synthesis. Proteins, enzymes, antibodies, compositions, etc., may be obtained, when available, from commercial sources, such as Sigma (U.S.A.). Exemplary methodologies for synthesizing (for example, fy using cDNA expression libraries or chemical synthesis of polypeptide followed by refolding into native proteins) or otherwise obtaining the proteins (or, for example, other polypeptides or compositions) for preparing the arrays are provided infra. Further, one skilled in the art would know that other well-known methodologies may also (or alternatively) be used. [0062]
  • Further, the first protein array which is deposited on the substrate need not be a single protein, but rather may be a plurality of different proteins having one or more PDZ domains. Similarly, the second protein which is applied to the protein array need not be a single protein, but rather may be a plurality of different proteins which comprise one or more amino acid sequences (S/T)-X-(V/I/L)-COOH. [0063]
  • Thus, the present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of first proteins, each first protein comprising a corresponding PDZ domain; and (b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the array of first proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein, for each of the first proteins, binding to the PDZ domain of the first protein. Each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0064]
  • The present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain; and (b) applying a plurality of second proteins, each of which comprises a corresponding amino acid sequence (S/T)-X-(V/I/L)-COOH, to corresponding elements of the first protein array, for each of the second proteins, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein in the corresponding array element. Each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. [0065]
  • The present disclosure also provides a method of preparing a protein array, comprising the steps of: (a) depositing on a substrate an array of a first polypeptide, the first polypeptide comprising a PDZ domain; and (b) applying a second polypeptide which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH to the first polypeptide array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second polypeptide binding to the PDZ domain of the first polypeptide. Each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group comprising the twenty naturally occurring amino acids. Further, the array may include an oligonucleotide, a sugar, messenger RNA and/or DNA. [0066]
  • The following exemplary embodiments and experimental details sections are set forth to aid in an understanding of the subject matter of this disclosure but are not intended to, and should not be construed to, limit in any way the invention as set forth in the claims which follow thereafter. [0067]
  • Exemplary Embodiments [0068]
  • Some embodiments of protein array preparation are described exemplarily below, with reference to FIGS. 13A-13C and [0069] 14A-14C, to illustrate some methodologies contemplated by the subject disclosure. One skilled in the art would recognize that these methodologies (and other aspects of the disclosure described herein) may be adapted for preparing arrays that include one or more other polypeptides, oligonucleotides, sugars, messenger RNAs, DNAs, and/or other compounds.
  • An array of first protein spots P is deposited on a substrate (for example, a glass slide) [FIG. 13A]. A second protein (A), which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, is applied to the first protein array [FIG. 13B]. The amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein. (A) binds to the PDZ domain of, the first protein (P) [FIG. 13C]. The protein array may be used to screen drugs X, Y, Z, etc. [0070]
  • According to one embodiment, a substrate comprising a glass plate and a plurality of microwells (FIG. 14C) formed by, for example, an enclosing hydrophobic Teflon mask may be used (see, for example, Mendoza, et al. 1999). The protein having a PDZ domain is dissolved in a buffered solution. The protein solution is then printed as an array on the substrate through, for example, a capillary-based print head attached to a X-Y-Z robot (or another type of microdispensing liquid handling robot system). By using an automated robotic system with the open microarray, a low-cost, highly parallel assay format is feasible. [0071]
  • The protein may also be printed onto a treated glass slide without wells (FIG. 14A). However, use of such a substrate has the disadvantage of having higher evaporation and a greater risk of cross contamination. [0072]
  • According to another embodiment, gels (and gel pads) may be used to immobilize the protein having a PDZ domain. Preparation of protein microchips using gel pads is described by, for example, Arenkov, et al. 2000. [0073]
  • For example, according to one embodiment using gel pads, the gel pads are deposited as a micromatrix on a glass slide (FIG. 14B) and then treated according to the composition of the gel pads (for example, photopolymerization may be used for polyacrylamide gel pads). The protein, which may be dissolved in a (for example, phosphate) buffered solution, is then transferred onto the gel pads, for example, via a pin by using a robot or a manual device. Preferably, the pin and micromatrix are kept at dew point to avoid evaporation of the protein solution. Next, the protein is chemically attached to the gels. Depending on the composition of the gel, any of a number of methodologies may be used. [0074]
  • An advantage of using gel support for fixation of biological compounds is its large capacity for immobilized compounds. In addition, the gel pads in the array are separated from each other by a hydrophobic surface. Therefore, gel pad arrays can be used as micro-test tubes to carry out specific interactions and chemical and enzymatic procedures with microchip substances. [0075]
  • Filter membranes also may be used to immobilize the protein. An appropriately selected membrane passively binds to, and thereby immobilizes, the protein, to produce protein filters. [0076]
  • In addition, the protein solution may be labeled by covalent linkage of a fluorecent dye to the amino groups on the protein. Fluorescence microscopy methodologies may be in conjunction with the protein-protein interaction (described exemplarily below), for example, to screen drug targets. [0077]
  • After an array of the first protein is deposited on the substrate through, for example, one of the methodologies described above, a second protein which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH is applied to the micromatrix. The amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binds to the PDZ domain of the first protein. The interaction between the first and second proteins is described below. After the second protein is applied, a wash may be applied. [0078]
  • The specific embodiments described herein are illustrative, and many variations can be introduced on these embodiments without departing from the spirit of the disclosure or from the scope of the appended claims. Elements and/or features of different illustrative embodiments may be combined with each other and/or substituted for each other, within the scope of this disclosure and appended claims. [0079]
  • For example, in some additional embodiments, the first protein which is deposited as an array on the substrate may comprise the amino acid sequence (S/T)-X-(V/I/L)-COOH, and the second protein which is applied to the first protein array may comprise the PDZ domain. [0080]
  • Additional variations to the embodiments described herein may be apparent to one of ordinary skill in the art from reading U.S. patent application Ser. Nos. 08/681,219 (filed Jul. 22, 1996) and 09/230,111 (filed May 17, 1999). The contents of U.S. Ser. Nos. 08/681,219 and 09/230,111 are hereby incorporated by reference. [0081]
  • Experimental methodologies and data in connection with the subject matter of this disclosure is illustrated in the Experimental Details section which follows. [0082]
  • First Series Of Experiments [0083]
  • Experimental Details [0084]
  • Methods and Materials [0085]
  • 1. Screening a Semi-Random and Random Peptide Library. [0086]
  • To create numerous mutations in a restricted DNA sequence, PCR mutagenesis with degenerate oligonucleotides was employed according to a protocol described elsewhere (Hill, et al.: 1987). Based on the homology-between human and rat, two palindromic sequences were designed for construction of semi-random library. The two primers used were 5′-CGGAATTCNNNNNNNNNAACAGCNNNNNNNNNAATGAANNNCAAAGTCTGNNNT GAGGATCCTCA-3′ (Seq. I.D. No. 31) and 5′-CGGAATTCGACTCAGAA NNNNNNAACTTCAGANNNNNNATCNNNNNNNNNGTCTGAGGATCCTCA-3′ (Seq. I.D. No. 32). Briefly, the two primers (each 200 pmol), purified by HPLC, were annealed at 70° C. for 5 minutes and cooled at 23° C. for 60 minutes. A klenow fragment (5 U) was used for filling in with a dNTP mix (final concentration, 1, mM per each dNTP) at 23° C. for 60 minutes. The reaction was stopped with 1 μl of 0.5 M EDTA and the DNA was purified with ethanol precipitation. The resulting double-stranded DNA was digested with EcoRI and BamHI and re-purified by electrophoresis on non-denaturing polyacrylamide gels. The double-strand oligonucleotides were then ligated into the EcoRI-BamHI sites of the pBTM116 plasmid. The ligation mixtures were electroporated into the [0087] E. coli XL1-Blue MRF′ (Stratagene) for the plasmid library. The large scale transformation was carried out as previously reported. The plasmid library was transformed into L40-strain cells (MATa, trp1, leu2, his3, ade2, LYS2: (lexAop)4-HIS3, URA3:: (lexAop)8-lacZ) carrying the plasmid pVP16-31 containing a FAP-1 cDNA (Sato, et al. 1995) Clones that formed on histidine-deficient medium (His+) were transferred to plates containing 40 μg/ml X-gal to test for a blue reaction product (β-gal+) in plate and filter assays., The clones selected by His+ and β-gal+ assay were tested for further analysis. The palindromic oligonucleotide, 5′-CGGAATTC-(NNN)4-1-TGAGGATCCTCA-3′ (Seq. I.D. No. 33), was used for the construction of the random peptide library.
  • 2. Synthesis of Peptides [0088]
  • Peptides were automatically synthesized on an Advanced ChemTech ACT357 by analogy to published procedures (Schnorrenberg and Gerhardt, 1989). Wang resin (0.2-0.3 mmole scale) was used for each run and N′-Fmoc protection was employed for all amino acids. Deprotection was achieved by treatment with 20% piperidine/DMF and coupling was completed using DIC/HOBt and subsequent HBTU/DIEA. After the last amino acid was coupled, the growing peptide on the resin was acetylated with Ac[0089] 2O/DMF. The peptide was cleaved from the resin with concomitant removal of all protecting groups by treating with TFA. The acetylated peptide was purified by HPLC and characterized by FAB-MS and 1H-NMR.
  • 3. Inhibition Asssay of Fas/FAP-1 Binding Using the C-[0090] Terminal 15 Amino Acids of Fas.
  • HFAP-10 cDNA (Sato, et al. 19-95) subcloned into the Bluescript vector pSK-II (Stratagene) was in vitro-translated from an internal methionine codon in the presence of [0091] 35S-L-methionine using a coupled in vitro transcription/translation system (Promega, TNT lysate) and T7 RNA polymerase. The resulting 35S-labeled protein was incubated with GST-Fas fusion proteins that, had been immobilized on GST-Sepharose 4B affinity beads (Pharmacia) in a buffer containing 150 mM NaCl, 50 mM Tris [pH 8.0], 5 mM DTT, 2 mM EDTA, 0.1% NP-40, 1 mM PMSF, 50 μg/ml leupeptin, 1 mM Benzamidine, and 7 μg/ml pepstatin for 16 hours at 4° C. After washing vigorously 4 times in the same buffer, associated proteins were recovered with the glutathione-Sepharose beads by centrifugation, eluted into boiling Laemmli buffer, and analyzed by SDS-PAGE and fluorography.
  • 4. Inhibition Assay of [0092] Terminal 15 Amino Acids of Fas and Inhibitory Effect of Fas/FAP-1 Binding Using Diverse Tripeptides.
  • In vitro-translated [[0093] 35S]HFAP-1 was purified with a NAP-5 column (Pharmacia) and incubated with 3 μM of GST-fusion proteins for 16 hours at 4° C. After washing 4 times in the binding buffer, radioactivity incorporation was determined in a β counter. The percentage of binding inhibition was calculated as follows: percent inhibition=[radioactivity incorporation using GST-Fas (191-335) with peptides radioactivity incorporation using GST-Fas (191-320) with peptides]/[radioactivity incorporation using GST-Fas (191-335) without peptides—radioactivity incorporation using GST-Fas (191-320) without peptides]. n=3.
  • 5. Interaction of the C-[0094] Terminal 3 Amino Acids of Fas With FAP-1 in Yeast and in Vitro.
  • The bait plasmids, pBTM116 (LexA)-SLV, -PLV, -SLY, and -SLA, were constructed and transformed into L40-strain with pVP16-FAP-1 or -ras. Six independent clones from each transformants were picked up for the analysis of growth on histidine-deficient medium. GST-Fas, -SLV, and PLV were purified with GST-Sepharose 4B affinity beads (Pharmacia). The methods for in vitro binding are described above. [0095]
  • 6. Immuno-Precipitation of Native Fas With GST-FAP-1 and Inhibition of Fas/FAP-1 Binding With Ac-SLV. [0096]
  • GST-fusion proteins with or without FAP-1 were incubated with cell extracts from Jurkat T-cells expressing Fas. The bound Fas was detected by Western analysis using anti-Fas monoclonal antibody (F22120, Transduction Laboratories). The tripeptides, Ac-SLV and Ac-SLY were used for the inhibition assay of Fas/FAP-1 binding. [0097]
  • 7. Microinjection of Ac-SLV Into the DLD-1 Cell Line. [0098]
  • DLD-1 human colon cancer cells were cultured in RPMI 1640 medium containing 10% FCS. For microinjection, cells were plated on CELLocate (Eppendorf) at 1×10[0099] 5 cells/2 ml in a 35 mm plastic culture dish and grown for 1 day. Just before microinjection, Fas monoclonal antibodies CH11 (MBL International) was added at the concentration of 500 ng/ml. All microinjection experiments were performed using an automatic microinjection system (Eppendorf transjector 5246, micro-manipulator 5171 and Femtotips) (Pantel, et al. 1995). Synthetic tripeptides were suspended in 0.1%. (w/v) FITC-Dextran (Sigma)/K-PBS at the concentration of 100 mM. The samples were microinjected into the cytoplasmic region of DLD-1 cells. Sixteen to 20 hours postinjection, the cells were washed with PBS and stained with 10 μg/ml Hoechst 33342 in PBS. After incubation at 37° C. for 30 minutes, the cells were photographed and the cells showing condensed chromatin were counted as apoptotic.
  • 8. Quantitation of Apoptosis in Microinjected DLD-1 Cells. [0100]
  • For each experiment, 25-100 cells were microinjected. Apoptosis of microinjected cells was determined by assessing morphological changes of chromatin using phase contrast and fluorescence microscopy (Wang, et al., 1995; McGahon, et al., 1995)., The data are means +/− S.D. for two or three independent determinations. [0101]
  • Discussion [0102]
  • In order to identify the minimal peptide stretch in the C-terminal region of the Fas receptor necessary for FAP-1 binding, an in vitro inhibition assay of Fas/FAP-1 binding was used using a series of synthetic peptides as well as yeast two-hybrid system peptide libraries (FIG. 2A) First, semi-random libraries (based on the homology between human and rat Fas) (FIGS. 2B and 2C) of 15 amino acids fused to a LexA DNA binding domain were constructed and co-transformed into yeast strain L40 with pVP16-31 (Sato, et al. 1995) that was originally isolated as FAP-1. After the selection of 200 His+colonies from an initial screen of 5.0×10[0103] 6 (Johnson, et al. 1986) transformants, 100 colonies that were β-galactosidase positive were picked for further analysis. Sequence analysis of the library plasmids encoding the C-terminal 15 amino acids revealed that all of the C-termini were either valine, leucine or isoleucine residues. Second, a random library of 4-15 amino acids fused to a LexA DNA binding domain was constructed and screened according to this strategy (FIG. 2D). Surprisingly, all of the third amino acid residues from the C-termini were serine, and the results of C-terminal amino acid analyses were identical to the screening of the semi-random cDNA libraries. No other significant amino acid sequences were found in these library screenings, suggesting that the motifs of the last three amino acids (tS-X-V/L/I) are very important for the association with the third PDZ domain of FAP-1 and play a crucial role in protein-protein interaction as well as for the regulation of Fas-induced apoptosis. To further confirm whether the last three amino acids are necessary and sufficient for Fas/FAP-1 binding, plasmids of the LexA-SLV, -PLV, -PLY, -SLY, and -SLA fusion proteins were constructed and co-transformed into yeast with pVP16-FAP-1. The results showed that only LexA-SLV associated with FAP-1, whereas LexA-PLV, -PLY, -SLY, and -SLA did not (FIG. 4A). In vitro binding studies using various GST-tripeptide fusions and in vitro-translated FAP-1 were consistent with these results (FIG. 4B).
  • In addition to yeast two-hybrid approaches, in vitro inhibition assay of Fas/FAP-1 binding was also used. First, a synthetic peptide of the C-[0104] terminal 15 amino acids was tested whether it could inhibit the binding of Fas and FAP-1 in vitro (FIG. 3A). The binding of in vitro-translated FAP-1 to GST-Fas was dramatically reduced and dependent on the concentration of the synthetic 15 amino acids of Fas. In contrast with these results, human PAMP peptide (Kitamura, et al. 1994) as a negative control had no effect on Fas/FAP-1 binding activity under the same biochemical conditions. Second, the effect of truncated C-terminal synthetic peptides of Fas on Fas/FAP-1 binding in vitro was examined. As shown in FIG. 3B, only the three C-terminal amino acids (Ac-SLV) were sufficient to obtain the same level of inhibitory effect on the binding of FAP-1 to Fas as achieved with the 4-15 synthetic peptides. Furthermore, Fas/FAP-1 binding was extensively investigated using the scanned tripeptides to determine the critical amino acids residues required for inhibition (FIG. 3C). The results revealed that the third amino acids residues from the C-terminus, and the C-terminal amino acids having the strongest inhibitory effect were either serine or threonine; and either valine, leucine, or isoleucine, respectively. However, there were no differences among the second amino acid residues from the C-terminus with respect to their inhibitory effect on Fas/FAP-1 binding. These results were consistent with those of the yeast two-hybrid system (FIGS. 2C and 2D). Therefore, it was concluded that the C-terminal three amino acids (SLV) are critical determinants of Fas binding to the third PDZ domain of FAP-1 protein.
  • To further substantiate that the PDZ domain interacts with tS/T-X-V/L/I under more native conditions, GST-fused FAP-1 proteins were tested for their ability to interact with Fas expressed in Jurkat T-cells. The results revealed that the tripeptide Ac-SLV, but not Ac-SLY, abolished in a dose-dependent manner the binding activity of FAP-1 to Fas proteins extracted from Jurkat T-cells (FIGS. 4C and 4D). This suggests that the C-terminal amino acids tSLV are the minimum binding site for FAP-1, and that the amino acids serine and valine are critical for this physical association. [0105]
  • To next examine the hypothesis that the physiological association between the C-terminal three amino acids of Fas and the third PDZ domain of FAP-1 is necessary for the in vivo function of FAP-1 as a negative regulator of Fas-mediated signal transduction, a microinjection experiment was employed with synthetic tripeptides in a colon cancer cell line, DLD-1, which expresses both Fas and FAP-1, and is resistant to Fas-induced apoptosis. The experiments involved the direct microinjection of the synthetic tripeptides into the cytoplasmic regions of single cells and the monitoring of the physiological response to Fas-induced apoptosis in vivo. The results showed that microinjection of Ac-SLV into DLD-1 cells dramatically induced apoptosis in the presence of Fas-monoclonal antibodies (CH11, 500 ng/ml) (FIGS. 5A, 5E and FIG. 6), but that microinjection of Ac-SLY and PBS/K did not (FIGS. 5B, 5F and FIG. 6). These results strongly support the hypothesis that the physical association of FAP-1 with the C-terminus of Fas is essential for protecting cells from Fas-induced apoptosis. [0106]
  • In summary, it was found that the C-terminal SLV of Fas is alone necessary and sufficient for binding to the third PDZ domain of FAP-1. Secondly, it is proposed that the new consensus motif of tS/T-X-V/L/I for such binding to the PDZ domain, instead of tS/T-X-V. It is therefore possible that FAP-1 plays important roles for the modulation of signal transduction pathways in addition to its physical, interaction with Fas. Thirdly, it is demonstrated that the targeted induction of Fas-mediated apoptosis in colon cancer cells by direct microinjection of the tripeptide Ac-SLV. Further investigations including the identification of a substrate(s) of FAP-1 and structure-function analysis will provide insight to the potential therapeutic applications of Fas/FAP-1 interaction in cancer as well as provide a better understanding of the inhibitory effect of FAP-1 on Fas-mediated signal transduction. [0107]
  • Second Series Of Experiments [0108]
  • FAP-1 was originally identified as a membrane-associated protein tyrosine phosphatase which binds to the C-terminus of Fas, and possesses six PDZ domains (also known as DHR domain or GLGF repeat). PDZ domain has recently-been shown as a novel module for specific protein-protein interaction, and it appears to be important in the assembly of membrane proteins and also in linking signaling molecules in a multiprotein complex. In recent comprehensive studies, it was found that the third PDZ domain of FAP-1 specifically recognized the sequence motif t(S/T)-X-V and interacts with the C-terminal three amino acids SLV of Fas (FIG. 9). In order to investigate the possibility that FAP-1 also interacts with the C-terminal region of p75NGFR (FIG. 8), an in vitro binding assay, was performed as well as, a yeast two-hybrid analysis by using a series of deletion mutants of p75NGFR. The results revealed that the C-terminal cytoplasmic region of p75NGFR, which is highly conserved among all species, interacts with FAP-1 (FIG. 10). Furthermore, the C-terminal three amino acids SPV of p75NGFR were necessary and sufficient for the interaction with the third PDZ domain of FAP-1 (FIGS. 11A and 11B) Since FAP-1 expression was found highest in fetal brain, these findings imply that interaction of FAP-1 with p75NGFR plays an important role for signal transduction pathway via p75NGFR in neuronal cells as well as in the formation of the initial signal-transducing complex for p75NGFR. [0109]
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  • 1 34 1 4 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 1 Xaa Leu Gly Xaa 1 2 9 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 2 Xaa Xaa Xaa Xaa Xaa Xaa Leu Gly Xaa 1 5 3 4 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 3 Ser Leu Gly Ile 1 4 3 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 4 Xaa Xaa Xaa 1 5 15 PRT human 5 Asp Ser Glu Asn Ser Asn Phe Arg Asn Glu Ile Gln Ser Leu Val 1 5 10 15 6 15 PRT rat 6 Ser Ile Ser Asn Ser Arg Asn Glu Asn Glu Gly Gln Ser Leu Glu 1 5 10 15 7 15 PRT mouse 7 Ser Thr Pro Asp Thr Gly Asn Glu Asn Glu Gly Gln Cys Leu Glu 1 5 10 15 8 4 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 8 Glu Ser Leu Val 1 9 6 PRT Artificial Sequence Description of Artificial Sequence sourcesynthesized 9 Thr Ile Gln Ser Val Ile 1 5 10 8 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 10 Arg Gly Phe Ile Ser Ser Leu Val 1 5 11 8 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 11 Arg Glu Thr Ile Glu Ser Thr Val 1 5 12 11 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 12 Gln Asn Phe Arg Thr Tyr Ile Val Ser Phe Val 1 5 10 13 13 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 13 Ser Asp Ser Asn Met Asn Met Asn Glu Leu Ser Glu Val 1 5 10 14 15 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 14 Pro Pro Thr Cys Ser Gln Ala Asn Ser Gly Arg Ile Ser Thr Leu 1 5 10 15 15 15 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 15 Ile Asp Leu Ala Ser Glu Phe Leu Phe Leu Ser Asn Ser Phe Leu 1 5 10 15 16 15 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 16 Asp Ser Glu Met Tyr Asn Phe Arg Ser Gln Leu Ala Ser Val Val 1 5 10 15 17 15 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 17 Ile Pro Pro Asp Ser Glu Asp Gly Asn Glu Glu Gln Ser Leu Val 1 5 10 15 18 4 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 18 Gln Ser Leu Val 1 19 5 PRT Artificial Sequence Description of Artificial Sequencesource synthesized 19 Ile Gln Ser Leu Val 1 5 20 6 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 20 Glu Ile Gln Ser Leu Val 1 5 21 7 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 21 Asn Glu Ile Gln Ser Leu Val 1 5 22 8 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 22 Arg Asn Glu Ile Gln Ser Leu Val 1 5 23 15 PRT Artificial Sequence Description of Artificial Sequencesourcesynthesized 23 Asp Ser Glu Asn Ser Asn Phe Arg Asn Glu Ile Gln Ser Leu Val 1 5 10 15 24 427 PRT human 24 Met Gly Ala Gly Ala Thr Gly Arg Ala Met Asp Gly Pro Arg Leu Leu 1 5 10 15 Leu Leu Leu Leu Leu Gly Val Ser Leu Gly Gly Ala Lys Glu Ala Cys 20 25 30 Pro Thr Gly Leu Tyr Thr His Ser Gly Glu Cys Cys Lys Ala Cys Asn 35 40 45 Leu Gly Glu Gly Val Ala Gln Pro Cys Gly Ala Asn Gln Thr Val Cys 50 55 60 Glu Pro Cys Leu Asp Ser Val Thr Phe Ser Asp Val Val Ser Ala Thr 65 70 75 80 Glu Pro Cys Lys Pro Cys Thr Glu Cys Val Gly Leu Gln Ser Met Ser 85 90 95 Ala Pro Cys Val Glu Ala Asp Asp Ala Val Cys Arg Cys Ala Tyr Gly 100 105 110 Tyr Tyr Gln Asp Glu Thr Thr Gly Arg Cys Glu Ala Cys Arg Val Cys 115 120 125 Glu Ala Gly Ser Gly Leu Val Phe Ser Cys Gln Asp Lys Gln Asn Thr 130 135 140 Val Cys Glu Glu Cys Pro Asp Gly Thr Tyr Ser Asp Glu Ala Asn His 145 150 155 160 Val Asp Pro Cys Leu Pro Cys Thr Val Cys Glu Asp Thr Glu Arg Gln 165 170 175 Leu Arg Glu Cys Thr Arg Trp Ala Asp Ala Glu Cys Glu Glu Ile Pro 180 185 190 Gly Arg Trp Ile Thr Arg Ser Thr Pro Pro Glu Gly Ser Asp Ser Thr 195 200 205 Ala Pro Ser Thr Gln Glu Pro Glu Ala Pro Pro Glu Gln Asp Leu Ile 210 215 220 Ala Ser Thr Val Ala Gly Val Val Thr Thr Val Met Gly Ser Ser Gln 225 230 235 240 Pro Val Val Thr Arg Gly Thr Thr Asp Asn Leu Ile Pro Val Tyr Cys 245 250 255 Ser Ile Leu Ala Ala Val Val Val Gly Leu Val Ala Tyr Ile Ala Phe 260 265 270 Lys Arg Trp Asn Ser Cys Lys Gln Asn Lys Gly Gly Ala Asn Ser Arg 275 280 285 Pro Val Asn Gln Thr Pro Pro Pro Glu Gly Glu Lys Ile His Ser Asp 290 295 300 Ser Gly Ile Ser Val Asp Ser Gln Ser Leu His Asp Gln Gln Pro His 305 310 315 320 Thr Gln Thr Ala Ser Gly Gln Ala Leu Lys Gly Asp Gly Gly Leu Tyr 325 330 335 Ser Ser Leu Pro Pro Ala Lys Arg Glu Glu Val Glu Lys Leu Leu Asn 340 345 350 Gly Ser Ala Gly Asp Thr Trp Arg His Leu Ala Gly Glu Leu Gly Tyr 355 360 365 Gln Pro Glu His Ile Asp Ser Phe Thr His Glu Ala Cys Pro Val Arg 370 375 380 Ala Leu Leu Ala Ser Trp Ala Thr Gln Asp Ser Ala Thr Leu Asp Ala 385 390 395 400 Leu Leu Ala Ala Leu Arg Arg Ile Gln Arg Ala Asp Leu Val Glu Ser 405 410 415 Leu Cys Ser Glu Ser Thr Ala Thr Ser Pro Val 420 425 25 458 PRT human 25 Met Asn Arg Gly Val Pro Phe Arg His Leu Leu Leu Val Leu Gln Leu 1 5 10 15 Ala Leu Leu Pro Ala Ala Thr Gln Gly Lys Lys Val Val Leu Gly Lys 20 25 30 Lys Gly Asp Thr Val Glu Leu Thr Cys Thr Ala Ser Gln Lys Lys Ser 35 40 45 Ile Gln Phe His Trp Lys Asn Ser Asn Gln Ile Lys Ile Leu Gly Asn 50 55 60 Gln Gly Ser Phe Leu Thr Lys Gly Pro Ser Lys Leu Asn Asp Arg Ala 65 70 75 80 Asp Ser Arg Arg Ser Leu Trp Asp Gln Gly Asn Phe Pro Leu Ile Ile 85 90 95 Lys Asn Leu Lys Ile Glu Asp Ser Asp Thr Tyr Ile Cys Glu Val Glu 100 105 110 Asp Gln Lys Glu Glu Val Gln Leu Leu Val Phe Gly Leu Thr Ala Asn 115 120 125 Ser Asp Thr His Leu Leu Gln Gly Gln Ser Leu Thr Ile Thr Leu Glu 130 135 140 Ser Pro Pro Gly Ser Ser Pro Ser Val Gln Cys Arg Ser Pro Arg Gly 145 150 155 160 Lys Asn Ile Gln Gly Gly Lys Thr Leu Ser Val Ser Gln Leu Glu Leu 165 170 175 Gln Asp Ser Gly Thr Trp Thr Cys Thr Val Leu Gln Asn Gln Lys Lys 180 185 190 Val Glu Phe Lys Ile Asp Ile Val Val Leu Ala Phe Gln Lys Ala Ser 195 200 205 Ser Ile Val Tyr Lys Lys Glu Gly Glu Gln Val Glu Phe Ser Phe Pro 210 215 220 Leu Ala Phe Thr Val Glu Lys Leu Thr Gly Ser Gly Glu Leu Trp Trp 225 230 235 240 Gln Ala Glu Arg Ala Ser Ser Ser Lys Ser Trp Ile Thr Phe Asp Leu 245 250 255 Lys Asn Lys Glu Val Ser Val Lys Arg Val Thr Gln Asp Pro Lys Leu 260 265 270 Gln Met Gly Lys Lys Leu Pro Leu His Leu Thr Leu Pro Gln Ala Leu 275 280 285 Pro Gln Tyr Ala Gly Ser Gly Asn Leu Thr Leu Ala Leu Glu Ala Lys 290 295 300 Thr Gly Lys Leu His Gln Glu Asn Val Leu Val Val Met Arg Ala Thr 305 310 315 320 Gln Leu Gln Lys Asn Leu Thr Cys Glu Val Trp Gly Pro Thr Ser Pro 325 330 335 Lys Leu Met Leu Ser Leu Lys Leu Glu Asn Lys Glu Ala Lys Val Ser 340 345 350 Lys Arg Glu Lys Ala Val Trp Val Leu Asn Pro Glu Ala Gly Met Trp 355 360 365 Gln Cys Leu Leu Ser Asp Ser Gly Gln Val Leu Leu Glu Ser Asn Ile 370 375 380 Lys Val Leu Pro Thr Trp Ser Thr Pro Val Gln Pro Met Ala Leu Ile 385 390 395 400 Val Leu Gly Gly Val Ala Gly Leu Leu Leu Phe Ile Gly Leu Gly Ile 405 410 415 Phe Phe Cys Val Arg Cys Arg His Arg Arg Arg Gln Ala Glu Arg Met 420 425 430 Ser Gln Ile Lys Arg Leu Leu Ser Glu Lys Lys Glu Cys Gln Cys Pro 435 440 445 His Arg Phe Gln Lys Thr Cys Ser Pro Ile 450 455 26 828 PRT human 26 Met Asn Ser Gly Val Ala Met Lys Tyr Gly Asn Asp Ser Ser Ala Glu 1 5 10 15 Leu Ser Glu Leu His Ser Ala Ala Leu Ala Ser Leu Lys Gly Asp Ile 20 25 30 Val Glu Leu Asn Lys Arg Leu Gln Gln Thr Glu Arg Glu Asp Leu Leu 35 40 45 Glu Lys Lys Leu Ala Lys Ala Gln Cys Glu Gln Ser His Leu Met Arg 50 55 60 Glu His Glu Asp Val Gln Glu Arg Thr Thr Leu Arg Tyr Glu Glu Arg 65 70 75 80 Ile Thr Glu Leu His Ser Val Ile Ala Glu Leu Asn Lys Lys Ile Asp 85 90 95 Arg Leu Gln Gly Thr Thr Ile Arg Glu Glu Asp Glu Tyr Ser Glu Leu 100 105 110 Arg Ser Glu Leu Ser Gln Ser Gln His Glu Val Asn Glu Asp Ser Arg 115 120 125 Ser Met Asp Gln Asp Gln Thr Ser Val Ser Ile Pro Glu Asn Gln Ser 130 135 140 Thr Met Val Thr Ala Asp Met Asp Asn Cys Ser Asp Ile Asn Ser Glu 145 150 155 160 Leu Gln Arg Val Leu Thr Gly Leu Glu Asn Val Val Cys Gly Arg Lys 165 170 175 Lys Ser Ser Cys Ser Leu Ser Val Ala Glu Val Asp Arg His Ile Glu 180 185 190 Gln Leu Thr Thr Ala Ser Glu His Cys Asp Leu Ala Ile Lys Thr Val 195 200 205 Glu Glu Ile Glu Gly Val Leu Gly Arg Asp Leu Tyr Pro Asn Leu Ala 210 215 220 Glu Glu Arg Ser Arg Trp Glu Lys Glu Leu Ala Gly Leu Arg Glu Glu 225 230 235 240 Asn Glu Ser Leu Thr Ala Met Leu Cys Ser Lys Glu Glu Glu Leu Asn 245 250 255 Arg Thr Lys Ala Thr Met Asn Ala Ile Arg Glu Glu Arg Asp Arg Leu 260 265 270 Arg Arg Arg Val Arg Glu Leu Gln Thr Arg Leu Gln Ser Val Gln Ala 275 280 285 Thr Gly Pro Ser Ser Pro Gly Arg Leu Thr Ser Thr Asn Arg Pro Ile 290 295 300 Asn Pro Ser Thr Gly Glu Leu Ser Thr Ser Ser Ser Ser Asn Asp Ile 305 310 315 320 Pro Ile Ala Lys Ile Ala Glu Arg Val Lys Leu Ser Lys Thr Arg Ser 325 330 335 Glu Ser Ser Ser Ser Asp Arg Pro Val Leu Gly Ser Glu Ile Ser Ser 340 345 350 Ile Gly Val Ser Ser Ser Val Ala Glu His Leu Ala His Ser Leu Gln 355 360 365 Asp Cys Ser Asn Ile Gln Glu Ile Phe Gln Thr Leu Tyr Ser His Gly 370 375 380 Ser Ala Ile Ser Glu Ser Lys Ile Arg Glu Phe Glu Val Glu Thr Glu 385 390 395 400 Arg Leu Asn Ser Arg Ile Glu His Leu Lys Ser Gln Asn Asp Leu Leu 405 410 415 Thr Ile Thr Leu Glu Glu Cys Lys Ser Asn Ala Glu Arg Met Ser Met 420 425 430 Leu Val Gly Lys Tyr Glu Ser Asn Ala Thr Ala Leu Arg Leu Ala Leu 435 440 445 Gln Tyr Ser Glu Gln Cys Ile Glu Ala Tyr Glu Leu Leu Leu Ala Leu 450 455 460 Ala Glu Ser Glu Gln Ser Leu Ile Leu Gly Gln Phe Arg Ala Ala Gly 465 470 475 480 Val Gly Ser Ser Pro Gly Asp Gln Ser Gly Asp Glu Asn Ile Thr Gln 485 490 495 Met Leu Lys Arg Ala His Asp Cys Arg Lys Thr Ala Glu Asn Ala Ala 500 505 510 Lys Ala Leu Leu Met Lys Leu Asp Gly Ser Cys Gly Gly Ala Phe Ala 515 520 525 Val Ala Gly Cys Ser Val Gln Pro Trp Glu Ser Leu Ser Ser Asn Ser 530 535 540 His Thr Ser Thr Thr Ser Ser Thr Ala Ser Ser Cys Asp Thr Glu Phe 545 550 555 560 Thr Lys Glu Asp Glu Gln Arg Leu Lys Asp Tyr Ile Gln Gln Leu Lys 565 570 575 Asn Asp Arg Ala Ala Val Lys Leu Thr Met Leu Glu Leu Glu Ser Ile 580 585 590 His Ile Asp Pro Leu Ser Tyr Asp Val Lys Pro Arg Gly Asp Ser Gln 595 600 605 Arg Leu Asp Leu Glu Asn Ala Val Leu Met Gln Glu Leu Met Ala Met 610 615 620 Lys Glu Glu Met Ala Glu Leu Lys Ala Gln Leu Tyr Leu Leu Glu Lys 625 630 635 640 Glu Lys Lys Ala Leu Glu Leu Lys Leu Ser Thr Arg Glu Ala Gln Glu 645 650 655 Gln Ala Tyr Leu Val His Ile Glu His Leu Lys Ser Glu Val Glu Glu 660 665 670 Gln Lys Glu Gln Arg Met Arg Ser Leu Ser Ser Thr Ser Ser Gly Ser 675 680 685 Lys Asp Lys Pro Gly Lys Glu Cys Ala Asp Ala Ala Ser Pro Ala Leu 690 695 700 Ser Leu Ala Glu Leu Arg Thr Thr Cys Ser Glu Asn Glu Leu Ala Ala 705 710 715 720 Glu Phe Thr Asn Ala Ile Arg Arg Glu Lys Lys Leu Lys Ala Arg Val 725 730 735 Gln Glu Leu Val Ser Ala Leu Glu Arg Leu Thr Lys Ser Ser Glu Ile 740 745 750 Arg His Gln Gln Ser Ala Glu Phe Val Asn Asp Leu Lys Arg Ala Asn 755 760 765 Ser Asn Leu Val Ala Ala Tyr Glu Lys Ala Lys Lys Lys His Gln Asn 770 775 780 Lys Leu Lys Lys Leu Glu Ser Gln Met Met Ala Met Val Glu Arg His 785 790 795 800 Glu Thr Gln Val Arg Met Leu Lys Gln Arg Ile Ala Leu Leu Glu Glu 805 810 815 Glu Asn Ser Arg Pro His Thr Asn Glu Thr Ser Leu 820 825 27 672 PRT human 27 Met Ala Asp Val Phe Pro Gly Asn Asp Ser Thr Ala Ser Gln Asp Val 1 5 10 15 Ala Asn Arg Phe Ala Arg Lys Gly Ala Leu Arg Gln Lys Asn Val His 20 25 30 Glu Val Lys Asp His Lys Phe Ile Ala Arg Phe Phe Lys Gln Pro Thr 35 40 45 Phe Cys Ser His Cys Thr Asp Phe Ile Trp Gly Phe Gly Lys Gly Gly 50 55 60 Phe Gln Cys Gln Val Cys Cys Phe Val Val His Lys Arg Cys His Glu 65 70 75 80 Phe Val Thr Phe Ser Cys Pro Gly Ala Asp Lys Gly Pro Asp Thr Asp 85 90 95 Asp Pro Arg Ser Lys His Lys Phe Lys Ile His Thr Tyr Gly Ser Pro 100 105 110 Thr Phe Cys Asp His Cys Gly Ser Leu Leu Tyr Gly Leu Ile His Gln 115 120 125 Gly Met Lys Cys Asp Thr Cys Asp Met Asn Val His Lys Gln Cys Val 130 135 140 Ile Asn Val Pro Ser Leu Cys Gly Met Asp His Thr Glu Lys Arg Gly 145 150 155 160 Arg Ile Tyr Leu Lys Ala Glu Val Ala Asp Glu Lys Leu His Val Thr 165 170 175 Val Arg Asp Ala Lys Asn Leu Ile Pro Met Asp Pro Asn Gly Leu Ser 180 185 190 Asp Pro Tyr Val Lys Leu Lys Leu Ile Pro Asp Pro Lys Asn Glu Ser 195 200 205 Lys Gln Lys Thr Lys Thr Ile Arg Ser Thr Leu Asn Pro Gln Trp Asn 210 215 220 Glu Ser Phe Thr Phe Lys Leu Lys Pro Ser Asp Lys Asp Arg Arg Leu 225 230 235 240 Ser Val Glu Ile Trp Asp Trp Asp Arg Thr Thr Arg Asn Asp Phe Met 245 250 255 Gly Ser Leu Ser Phe Gly Val Ser Glu Leu Met Lys Met Pro Ala Ser 260 265 270 Gly Trp Tyr Lys Leu Leu Asn Gln Glu Glu Gly Glu Tyr Tyr Asn Val 275 280 285 Pro Ile Pro Glu Gly Asp Glu Glu Gly Asn Met Glu Leu Arg Gln Lys 290 295 300 Phe Glu Lys Ala Lys Leu Gly Pro Ala Gly Asn Lys Val Ile Ser Pro 305 310 315 320 Ser Glu Asp Arg Lys Gln Pro Ser Asn Asn Leu Asp Arg Val Lys Leu 325 330 335 Thr Asp Phe Asn Phe Leu Met Val Leu Gly Lys Gly Ser Phe Gly Lys 340 345 350 Val Met Leu Ala Asp Arg Lys Gly Thr Glu Glu Leu Tyr Ala Ile Lys 355 360 365 Ile Leu Lys Lys Asp Val Val Ile Gln Asp Asp Asp Val Glu Cys Thr 370 375 380 Met Val Glu Lys Arg Val Leu Ala Leu Leu Asp Lys Pro Pro Phe Leu 385 390 395 400 Thr Gln Leu His Ser Cys Phe Gln Thr Val Asp Arg Leu Tyr Phe Val 405 410 415 Met Glu Tyr Val Asn Gly Gly Asp Leu Met Tyr His Ile Gln Gln Val 420 425 430 Gly Lys Phe Lys Glu Pro Gln Ala Val Phe Tyr Ala Ala Glu Ile Ser 435 440 445 Ile Gly Leu Phe Phe Leu His Lys Arg Gly Ile Ile Tyr Arg Asp Leu 450 455 460 Lys Leu Asp Asn Val Met Leu Asp Ser Glu Gly His Ile Lys Ile Ala 465 470 475 480 Asp Phe Gly Met Cys Lys Glu His Met Met Asp Gly Val Thr Thr Arg 485 490 495 Thr Phe Cys Gly Thr Pro Asp Tyr Ile Ala Pro Glu Ile Ile Ala Tyr 500 505 510 Gln Pro Tyr Gly Lys Ser Val Asp Trp Trp Ala Tyr Gly Val Leu Leu 515 520 525 Tyr Glu Met Leu Ala Gly Gln Pro Pro Phe Asp Gly Glu Asp Glu Asp 530 535 540 Glu Leu Phe Gln Ser Ile Met Glu His Asn Val Ser Tyr Pro Lys Ser 545 550 555 560 Leu Ser Lys Glu Ala Val Ser Ile Cys Lys Gly Leu Met Thr Lys His 565 570 575 Pro Ala Lys Arg Leu Gly Cys Gly Pro Glu Gly Glu Arg Asp Val Arg 580 585 590 Glu His Ala Phe Phe Arg Arg Ile Asp Trp Glu Lys Leu Glu Asn Arg 595 600 605 Glu Ile Gln Pro Pro Phe Lys Pro Lys Val Cys Gly Lys Gly Ala Glu 610 615 620 Asn Phe Asp Lys Phe Phe Thr Arg Gly Gln Pro Val Leu Thr Pro Pro 625 630 635 640 Asp Gln Leu Val Ile Ala Asn Ile Asp Gln Ser Asp Phe Glu Gly Phe 645 650 655 Ser Tyr Val Asn Pro Gln Phe Val His Pro Ile Leu Gln Ser Ala Val 660 665 670 28 471 PRT human 28 Met Asp Ile Leu Cys Glu Glu Asn Thr Ser Leu Ser Ser Thr Thr Asn 1 5 10 15 Ser Leu Met Gln Leu Asn Asp Asp Thr Arg Leu Tyr Ser Asn Asp Phe 20 25 30 Asn Ser Gly Glu Ala Asn Thr Ser Asp Ala Phe Asn Trp Thr Val Asp 35 40 45 Ser Glu Asn Arg Thr Asn Leu Ser Cys Glu Gly Cys Leu Ser Pro Ser 50 55 60 Cys Leu Ser Leu Leu His Leu Gln Glu Lys Asn Trp Ser Ala Leu Leu 65 70 75 80 Thr Ala Val Val Ile Ile Leu Thr Ile Ala Gly Asn Ile Leu Val Ile 85 90 95 Met Ala Val Ser Leu Glu Lys Lys Leu Gln Asn Ala Thr Asn Tyr Phe 100 105 110 Leu Met Ser Leu Ala Ile Ala Asp Met Leu Leu Gly Phe Leu Val Met 115 120 125 Pro Val Ser Met Leu Thr Ile Leu Tyr Gly Tyr Arg Trp Pro Leu Pro 130 135 140 Ser Lys Leu Cys Ala Val Trp Ile Tyr Leu Asp Val Leu Phe Ser Thr 145 150 155 160 Ala Ser Ile Met His Leu Cys Ala Ile Ser Leu Asp Arg Tyr Val Ala 165 170 175 Ile Gln Asn Pro Ile His His Ser Arg Phe Asn Ser Arg Thr Lys Ala 180 185 190 Phe Leu Lys Ile Ile Ala Val Trp Thr Ile Ser Val Gly Ile Ser Met 195 200 205 Pro Ile Pro Val Phe Gly Leu Gln Asp Asp Ser Lys Val Phe Lys Glu 210 215 220 Gly Ser Cys Leu Leu Ala Asp Asp Asn Phe Val Leu Ile Gly Ser Phe 225 230 235 240 Val Ser Phe Phe Ile Pro Leu Thr Ile Met Val Ile Thr Tyr Phe Leu 245 250 255 Thr Ile Lys Ser Leu Gln Lys Glu Ala Thr Leu Cys Val Ser Asp Leu 260 265 270 Gly Thr Arg Ala Lys Leu Ala Ser Phe Ser Phe Leu Pro Gln Ser Ser 275 280 285 Leu Ser Ser Glu Lys Leu Phe Gln Arg Ser Ile His Arg Glu Pro Gly 290 295 300 Ser Tyr Thr Gly Arg Arg Thr Met Gln Ser Ile Ser Asn Glu Gln Lys 305 310 315 320 Ala Cys Lys Val Leu Gly Ile Val Phe Phe Leu Phe Val Val Met Trp 325 330 335 Cys Pro Phe Phe Ile Thr Asn Ile Met Ala Val Ile Cys Lys Glu Ser 340 345 350 Cys Asn Glu Asp Val Ile Gly Ala Leu Leu Asn Val Phe Val Trp Ile 355 360 365 Gly Tyr Leu Ser Ser Ala Val Asn Pro Leu Val Tyr Thr Leu Phe Asn 370 375 380 Lys Thr Tyr Arg Ser Ala Phe Ser Arg Tyr Ile Gln Cys Gln Tyr Lys 385 390 395 400 Glu Asn Lys Lys Pro Leu Gln Leu Ile Leu Val Asn Thr Ile Pro Ala 405 410 415 Leu Ala Tyr Lys Ser Ser Gln Leu Gln Met Gly Gln Lys Lys Asn Ser 420 425 430 Lys Gln Asp Ala Lys Thr Thr Asp Asn Asp Cys Ser Met Val Ala Leu 435 440 445 Gly Lys Gln His Ser Glu Glu Ala Ser Lys Asp Asn Ser Asp Gly Val 450 455 460 Asn Glu Lys Val Ser Cys Val 465 470 29 481 PRT human 29 Met Ala Leu Ser Tyr Arg Val Ser Glu Leu Gln Ser Thr Ile Pro Glu 1 5 10 15 His Ile Leu Gln Ser Thr Phe Val His Val Ile Ser Ser Asn Trp Ser 20 25 30 Gly Leu Gln Thr Glu Ser Ile Pro Glu Glu Met Lys Gln Ile Val Glu 35 40 45 Glu Gln Gly Asn Lys Leu His Trp Ala Ala Leu Leu Ile Leu Met Val 50 55 60 Ile Ile Pro Thr Ile Gly Gly Asn Thr Leu Val Ile Leu Ala Val Ser 65 70 75 80 Leu Glu Lys Lys Leu Gln Tyr Ala Thr Asn Tyr Phe Leu Met Ser Leu 85 90 95 Ala Val Ala Asp Leu Leu Val Gly Leu Phe Val Met Pro Ile Ala Leu 100 105 110 Leu Thr Ile Met Phe Glu Ala Met Trp Pro Leu Pro Leu Val Leu Cys 115 120 125 Pro Ala Trp Leu Phe Leu Asp Val Leu Phe Ser Thr Ala Ser Ile Met 130 135 140 His Leu Cys Ala Ile Ser Val Asp Arg Tyr Ile Ala Ile Lys Lys Pro 145 150 155 160 Ile Gln Ala Asn Gln Tyr Asn Ser Arg Ala Thr Ala Phe Ile Lys Ile 165 170 175 Thr Val Val Trp Leu Ile Ser Ile Gly Ile Ala Ile Pro Val Pro Ile 180 185 190 Lys Gly Ile Glu Thr Asp Val Asp Asn Pro Asn Asn Ile Thr Cys Val 195 200 205 Leu Thr Lys Glu Arg Phe Gly Asp Phe Met Leu Phe Gly Ser Leu Ala 210 215 220 Ala Phe Phe Thr Pro Leu Ala Ile Met Ile Val Thr Tyr Phe Leu Thr 225 230 235 240 Ile His Ala Leu Gln Lys Lys Ala Tyr Leu Val Lys Asn Lys Pro Pro 245 250 255 Gln Arg Leu Thr Trp Leu Thr Val Ser Thr Val Phe Gln Arg Asp Glu 260 265 270 Thr Pro Cys Ser Ser Pro Glu Lys Val Ala Met Leu Asp Gly Ser Arg 275 280 285 Lys Asp Lys Ala Leu Pro Asn Ser Gly Asp Glu Thr Leu Met Arg Arg 290 295 300 Thr Ser Thr Ile Gly Lys Lys Ser Val Gln Thr Ile Ser Asn Glu Gln 305 310 315 320 Arg Ala Ser Lys Val Leu Gly Ile Val Phe Phe Leu Phe Leu Leu Met 325 330 335 Trp Cys Pro Phe Phe Ile Thr Asn Ile Thr Leu Val Leu Cys Asp Ser 340 345 350 Cys Asn Gln Thr Thr Leu Gln Met Leu Leu Glu Ile Phe Val Trp Ile 355 360 365 Gly Tyr Val Ser Ser Gly Val Asn Pro Leu Val Tyr Thr Leu Phe Asn 370 375 380 Lys Thr Phe Arg Asp Ala Phe Gly Arg Tyr Ile Thr Cys Asn Tyr Arg 385 390 395 400 Ala Thr Lys Ser Val Lys Thr Leu Arg Lys Arg Ser Ser Lys Ile Tyr 405 410 415 Phe Arg Asn Pro Met Ala Glu Asn Ser Lys Phe Phe Lys Lys His Gly 420 425 430 Ile Arg Asn Gly Ile Asn Pro Ala Met Tyr Gln Ser Pro Met Arg Leu 435 440 445 Arg Ser Ser Thr Ile Gln Ser Ser Ser Ile Ile Leu Leu Asp Thr Leu 450 455 460 Leu Leu Thr Glu Asn Glu Gly Asp Lys Thr Glu Glu Gln Val Ser Tyr 465 470 475 480 Val 30 2843 PRT human 30 Met Ala Ala Ala Ser Tyr Asp Gln Leu Leu Lys Gln Val Glu Ala Leu 1 5 10 15 Lys Met Glu Asn Ser Asn Leu Arg Gln Glu Leu Glu Asp Asn Ser Asn 20 25 30 His Leu Thr Lys Leu Glu Thr Glu Ala Ser Asn Met Lys Glu Val Leu 35 40 45 Lys Gln Leu Gln Gly Ser Ile Glu Asp Glu Ala Met Ala Ser Ser Gly 50 55 60 Gln Ile Asp Leu Leu Glu Arg Leu Lys Glu Leu Asn Leu Asp Ser Ser 65 70 75 80 Asn Phe Pro Gly Val Lys Leu Arg Ser Lys Met Ser Leu Arg Ser Tyr 85 90 95 Gly Ser Arg Glu Gly Ser Val Ser Ser Arg Ser Gly Glu Cys Ser Pro 100 105 110 Val Pro Met Gly Ser Phe Pro Arg Arg Gly Phe Val Asn Gly Ser Arg 115 120 125 Glu Ser Thr Gly Tyr Leu Glu Glu Leu Glu Lys Glu Arg Ser Leu Leu 130 135 140 Leu Ala Asp Leu Asp Lys Glu Glu Lys Glu Lys Asp Trp Tyr Tyr Ala 145 150 155 160 Gln Leu Gln Asn Leu Thr Lys Arg Ile Asp Ser Leu Pro Leu Thr Glu 165 170 175 Asn Phe Ser Leu Gln Thr Asp Met Thr Arg Arg Gln Leu Glu Tyr Glu 180 185 190 Ala Arg Gln Ile Arg Val Ala Met Glu Glu Gln Leu Gly Thr Cys Gln 195 200 205 Asp Met Glu Lys Arg Ala Gln Arg Arg Ile Ala Arg Ile Gln Gln Ile 210 215 220 Glu Lys Asp Ile Leu Arg Ile Arg Gln Leu Leu Gln Ser Gln Ala Thr 225 230 235 240 Glu Ala Glu Arg Ser Ser Gln Asn Lys His Glu Thr Gly Ser His Asp 245 250 255 Ala Glu Arg Gln Asn Glu Gly Gln Gly Val Gly Glu Ile Asn Met Ala 260 265 270 Thr Ser Gly Asn Gly Gln Gly Ser Thr Thr Arg Met Asp His Glu Thr 275 280 285 Ala Ser Val Leu Ser Ser Ser Ser Thr His Ser Ala Pro Arg Arg Leu 290 295 300 Thr Ser His Leu Gly Thr Lys Val Glu Met Val Tyr Ser Leu Leu Ser 305 310 315 320 Met Leu Gly Thr His Asp Lys Asp Asp Met Ser Arg Thr Leu Leu Ala 325 330 335 Met Ser Ser Ser Gln Asp Ser Cys Ile Ser Met Arg Gln Ser Gly Cys 340 345 350 Leu Pro Leu Leu Ile Gln Leu Leu His Gly Asn Asp Lys Asp Ser Val 355 360 365 Leu Leu Gly Asn Ser Arg Gly Ser Lys Glu Ala Arg Ala Arg Ala Ser 370 375 380 Ala Ala Leu His Asn Ile Ile His Ser Gln Pro Asp Asp Lys Arg Gly 385 390 395 400 Arg Arg Glu Ile Arg Val Leu His Leu Leu Glu Gln Ile Arg Ala Tyr 405 410 415 Cys Ser Thr Cys Trp Glu Trp Gln Glu Ala His Glu Pro Gly Met Asp 420 425 430 Gln Asp Lys Asn Pro Met Pro Ala Pro Val Glu His Gln Ile Cys Pro 435 440 445 Ala Val Cys Val Leu Met Lys Leu Ser Phe Asp Glu Glu His Arg His 450 455 460 Ala Met Asn Glu Leu Gly Gly Leu Gln Ala Ile Ala Glu Leu Leu Gln 465 470 475 480 Val Asp Cys Glu Met Tyr Gly Leu Thr Asn Asp His Tyr Ser Ile Thr 485 490 495 Leu Arg Arg Tyr Ala Gly Met Ala Leu Thr Asn Leu Thr Phe Gly Asp 500 505 510 Val Ala Asn Lys Ala Thr Leu Cys Ser Met Lys Gly Cys Met Arg Ala 515 520 525 Leu Val Ala Gln Leu Lys Ser Glu Ser Glu Asp Leu Gln Gln Val Ile 530 535 540 Ala Ser Val Leu Arg Asn Leu Ser Trp Arg Ala Asp Val Asn Ser Lys 545 550 555 560 Lys Thr Leu Arg Glu Val Gly Ser Val Lys Ala Leu Met Glu Cys Ala 565 570 575 Leu Glu Val Lys Lys Glu Ser Thr Leu Lys Ser Val Leu Ser Ala Leu 580 585 590 Trp Asn Leu Ser Ala His Cys Thr Glu Asn Lys Ala Asp Ile Cys Ala 595 600 605 Val Asp Gly Ala Leu Ala Phe Leu Val Gly Thr Leu Thr Tyr Arg Ser 610 615 620 Gln Thr Asn Thr Leu Ala Ile Ile Glu Ser Gly Gly Gly Ile Leu Arg 625 630 635 640 Asn Val Ser Ser Leu Ile Ala Thr Asn Glu Asp His Arg Gln Ile Leu 645 650 655 Arg Glu Asn Asn Cys Leu Gln Thr Leu Leu Gln His Leu Lys Ser His 660 665 670 Ser Leu Thr Ile Val Ser Asn Ala Cys Gly Thr Leu Trp Asn Leu Ser 675 680 685 Ala Arg Asn Pro Lys Asp Gln Glu Ala Leu Trp Asp Met Gly Ala Val 690 695 700 Ser Met Leu Lys Asn Leu Ile His Ser Lys His Lys Met Ile Ala Met 705 710 715 720 Gly Ser Ala Ala Ala Leu Arg Asn Leu Met Ala Asn Arg Pro Ala Lys 725 730 735 Tyr Lys Asp Ala Asn Ile Met Ser Pro Gly Ser Ser Leu Pro Ser Leu 740 745 750 His Val Arg Lys Gln Lys Ala Leu Glu Ala Glu Leu Asp Ala Gln His 755 760 765 Leu Ser Glu Thr Phe Asp Asn Ile Asp Asn Ile Ser Pro Lys Ala Ser 770 775 780 His Arg Ser Lys Gln Arg His Lys Gln Ser Leu Tyr Gly Asp Tyr Val 785 790 795 800 Phe Asp Thr Asn Arg His Asp Asp Asn Arg Ser Asp Asn Phe Asn Thr 805 810 815 Gly Asn Met Thr Val Leu Ser Pro Tyr Leu Asn Thr Thr Val Leu Pro 820 825 830 Ser Ser Ser Ser Ser Arg Gly Ser Leu Asp Ser Ser Arg Ser Glu Lys 835 840 845 Asp Arg Ser Leu Glu Arg Glu Arg Gly Ile Gly Leu Gly Asn Tyr His 850 855 860 Pro Ala Thr Glu Asn Pro Gly Thr Ser Ser Lys Arg Gly Leu Gln Ile 865 870 875 880 Ser Thr Thr Ala Ala Gln Ile Ala Lys Val Met Glu Glu Val Ser Ala 885 890 895 Ile His Thr Ser Gln Glu Asp Arg Ser Ser Gly Ser Thr Thr Glu Leu 900 905 910 His Cys Val Thr Asp Glu Arg Asn Ala Leu Arg Arg Ser Ser Ala Ala 915 920 925 His Thr His Ser Asn Thr Tyr Asn Phe Thr Lys Ser Glu Asn Ser Asn 930 935 940 Arg Thr Cys Ser Met Pro Tyr Ala Lys Leu Glu Tyr Lys Arg Ser Ser 945 950 955 960 Asn Asp Ser Leu Asn Ser Val Ser Ser Ser Asp Gly Tyr Gly Lys Arg 965 970 975 Gly Gln Met Lys Pro Ser Ile Glu Ser Tyr Ser Glu Asp Asp Glu Ser 980 985 990 Lys Phe Cys Ser Tyr Gly Gln Tyr Pro Ala Asp Leu Ala His Lys Ile 995 1000 1005 His Ser Ala Asn His Met Asp Asp Asn Asp Gly Glu Leu Asp Thr Pro 1010 1015 1020 Ile Asn Tyr Ser Leu Lys Tyr Ser Asp Glu Gln Leu Asn Ser Gly Arg 1025 1030 1035 1040 Gln Ser Pro Ser Gln Asn Glu Arg Trp Ala Arg Pro Lys His Ile Ile 1045 1050 1055 Glu Asp Glu Ile Lys Gln Ser Glu Gln Arg Gln Ser Arg Asn Gln Ser 1060 1065 1070 Thr Thr Tyr Pro Val Tyr Thr Glu Ser Thr Asp Asp Lys His Leu Lys 1075 1080 1085 Phe Gln Pro His Phe Gly Gln Gln Glu Cys Val Ser Pro Tyr Arg Ser 1090 1095 1100 Arg Gly Ala Asn Gly Ser Glu Thr Asn Arg Val Gly Ser Asn His Gly 1105 1110 1115 1120 Ile Asn Gln Asn Val Ser Gln Ser Leu Cys Gln Glu Asp Asp Tyr Glu 1125 1130 1135 Asp Asp Lys Pro Thr Asn Tyr Ser Glu Arg Tyr Ser Glu Glu Glu Gln 1140 1145 1150 His Glu Glu Glu Glu Arg Pro Thr Asn Tyr Ser Ile Lys Tyr Asn Glu 1155 1160 1165 Glu Lys Arg His Val Asp Gln Pro Ile Asp Tyr Ser Ile Leu Lys Ala 1170 1175 1180 Thr Asp Ile Pro Ser Ser Gln Lys Gln Ser Phe Ser Phe Ser Lys Ser 1185 1190 1195 1200 Ser Ser Gly Gln Ser Ser Lys Thr Glu His Met Ser Ser Ser Ser Glu 1205 1210 1215 Asn Thr Ser Thr Pro Ser Ser Asn Ala Lys Arg Gln Asn Gln Leu His 1220 1225 1230 Pro Ser Ser Ala Gln Ser Arg Ser Gly Gln Pro Gln Lys Ala Ala Thr 1235 1240 1245 Cys Lys Val Ser Ser Ile Asn Gln Glu Thr Ile Gln Thr Tyr Cys Val 1250 1255 1260 Glu Asp Thr Pro Ile Cys Phe Ser Arg Cys Ser Ser Leu Ser Ser Leu 1265 1270 1275 1280 Ser Ser Ala Glu Asp Glu Ile Gly Cys Asn Gln Thr Thr Gln Glu Ala 1285 1290 1295 Asp Ser Ala Asn Thr Leu Gln Ile Ala Glu Ile Lys Glu Lys Ile Gly 1300 1305 1310 Thr Arg Ser Ala Glu Asp Pro Val Ser Glu Val Pro Ala Val Ser Gln 1315 1320 1325 His Pro Arg Thr Lys Ser Ser Arg Leu Gln Gly Ser Ser Leu Ser Ser 1330 1335 1340 Glu Ser Ala Arg His Lys Ala Val Glu Phe Ser Ser Gly Ala Lys Ser 1345 1350 1355 1360 Pro Ser Lys Ser Gly Ala Gln Thr Pro Lys Ser Pro Pro Glu His Tyr 1365 1370 1375 Val Gln Glu Thr Pro Leu Met Phe Ser Arg Cys Thr Ser Val Ser Ser 1380 1385 1390 Leu Asp Ser Phe Glu Ser Arg Ser Ile Ala Ser Ser Val Gln Ser Glu 1395 1400 1405 Pro Cys Ser Gly Met Val Ser Gly Ile Ile Ser Pro Ser Asp Leu Pro 1410 1415 1420 Asp Ser Pro Gly Gln Thr Met Pro Pro Ser Arg Ser Lys Thr Pro Pro 1425 1430 1435 1440 Pro Pro Pro Gln Thr Ala Gln Thr Lys Arg Glu Val Pro Lys Asn Lys 1445 1450 1455 Ala Pro Thr Ala Glu Lys Arg Glu Ser Gly Pro Lys Gln Ala Ala Val 1460 1465 1470 Asn Ala Ala Val Gln Arg Val Gln Val Leu Pro Asp Ala Asp Thr Leu 1475 1480 1485 Leu His Phe Ala Thr Glu Ser Thr Pro Asp Gly Phe Ser Cys Ser Ser 1490 1495 1500 Ser Leu Ser Ala Leu Ser Leu Asp Glu Pro Phe Ile Gln Lys Asp Val 1505 1510 1515 1520 Glu Leu Arg Ile Met Pro Pro Val Gln Glu Asn Asp Asn Gly Asn Glu 1525 1530 1535 Thr Glu Ser Glu Gln Pro Lys Glu Ser Asn Glu Asn Gln Glu Lys Glu 1540 1545 1550 Ala Glu Lys Thr Ile Asp Ser Glu Lys Asp Leu Leu Asp Asp Ser Asp 1555 1560 1565 Asp Asp Asp Ile Glu Ile Leu Glu Glu Cys Ile Ile Ser Ala Met Pro 1570 1575 1580 Thr Lys Ser Ser Arg Lys Ala Lys Lys Pro Ala Gln Thr Ala Ser Lys 1585 1590 1595 1600 Leu Pro Pro Pro Val Ala Arg Lys Pro Ser Gln Leu Pro Val Tyr Lys 1605 1610 1615 Leu Leu Pro Ser Gln Asn Arg Leu Gln Pro Gln Lys His Val Ser Phe 1620 1625 1630 Thr Pro Gly Asp Asp Met Pro Arg Val Tyr Cys Val Glu Gly Thr Pro 1635 1640 1645 Ile Asn Phe Ser Thr Ala Thr Ser Leu Ser Asp Leu Thr Ile Glu Ser 1650 1655 1660 Pro Pro Asn Glu Leu Ala Ala Gly Glu Gly Val Arg Gly Gly Ala Gln 1665 1670 1675 1680 Ser Gly Glu Phe Glu Lys Arg Asp Thr Ile Pro Thr Glu Gly Arg Ser 1685 1690 1695 Thr Asp Glu Ala Gln Gly Gly Lys Thr Ser Ser Val Thr Ile Pro Glu 1700 1705 1710 Leu Asp Asp Asn Lys Ala Glu Glu Gly Asp Ile Leu Ala Glu Cys Ile 1715 1720 1725 Asn Ser Ala Met Pro Lys Gly Lys Ser His Lys Pro Phe Arg Val Lys 1730 1735 1740 Lys Ile Met Asp Gln Val Gln Gln Ala Ser Ala Ser Ser Ser Ala Pro 1745 1750 1755 1760 Asn Lys Asn Gln Leu Asp Gly Lys Lys Lys Lys Pro Thr Ser Pro Val 1765 1770 1775 Lys Pro Ile Pro Gln Asn Thr Glu Tyr Arg Thr Arg Val Arg Lys Asn 1780 1785 1790 Ala Asp Ser Lys Asn Asn Leu Asn Ala Glu Arg Val Phe Ser Asp Asn 1795 1800 1805 Lys Asp Ser Lys Lys Gln Asn Leu Lys Asn Asn Ser Lys Asp Phe Asn 1810 1815 1820 Asp Lys Leu Pro Asn Asn Glu Asp Arg Val Arg Gly Ser Phe Ala Phe 1825 1830 1835 1840 Asp Ser Pro His His Tyr Thr Pro Ile Glu Gly Thr Pro Tyr Cys Phe 1845 1850 1855 Ser Arg Asn Asp Ser Leu Ser Ser Leu Asp Phe Asp Asp Asp Asp Val 1860 1865 1870 Asp Leu Ser Arg Glu Lys Ala Glu Leu Arg Lys Ala Lys Glu Asn Lys 1875 1880 1885 Glu Ser Glu Ala Lys Val Thr Ser His Thr Glu Leu Thr Ser Asn Gln 1890 1895 1900 Gln Ser Ala Asn Lys Thr Gln Ala Ile Ala Lys Gln Pro Ile Asn Arg 1905 1910 1915 1920 Gly Gln Pro Lys Pro Ile Leu Gln Lys Gln Ser Thr Phe Pro Gln Ser 1925 1930 1935 Ser Lys Asp Ile Pro Asp Arg Gly Ala Ala Thr Asp Glu Lys Leu Gln 1940 1945 1950 Asn Phe Ala Ile Glu Asn Thr Pro Val Cys Phe Ser His Asn Ser Ser 1955 1960 1965 Leu Ser Ser Leu Ser Asp Ile Asp Gln Glu Asn Asn Asn Lys Glu Asn 1970 1975 1980 Glu Pro Ile Lys Glu Thr Glu Pro Pro Asp Ser Gln Gly Glu Pro Ser 1985 1990 1995 2000 Lys Pro Gln Ala Ser Gly Tyr Ala Pro Lys Ser Phe His Val Glu Asp 2005 2010 2015 Thr Pro Val Cys Phe Ser Arg Asn Ser Ser Leu Ser Ser Leu Ser Ile 2020 2025 2030 Asp Ser Glu Asp Asp Leu Leu Gln Glu Cys Ile Ser Ser Ala Met Pro 2035 2040 2045 Lys Lys Lys Lys Pro Ser Arg Leu Lys Gly Asp Asn Glu Lys His Ser 2050 2055 2060 Pro Arg Asn Met Gly Gly Ile Leu Gly Glu Asp Leu Thr Leu Asp Leu 2065 2070 2075 2080 Lys Asp Ile Gln Arg Pro Asp Ser Glu His Gly Leu Ser Pro Asp Ser 2085 2090 2095 Glu Asn Phe Asp Trp Lys Ala Ile Gln Glu Gly Ala Asn Ser Ile Val 2100 2105 2110 Ser Ser Leu His Gln Ala Ala Ala Ala Ala Cys Leu Ser Arg Gln Ala 2115 2120 2125 Ser Ser Asp Ser Asp Ser Ile Leu Ser Leu Lys Ser Gly Ile Ser Leu 2130 2135 2140 Gly Ser Pro Phe His Leu Thr Pro Asp Gln Glu Glu Lys Pro Phe Thr 2145 2150 2155 2160 Ser Asn Lys Gly Pro Arg Ile Leu Lys Pro Gly Glu Lys Ser Thr Leu 2165 2170 2175 Glu Thr Lys Lys Ile Glu Ser Glu Ser Lys Gly Ile Lys Gly Gly Lys 2180 2185 2190 Lys Val Tyr Lys Ser Leu Ile Thr Gly Lys Val Arg Ser Asn Ser Glu 2195 2200 2205 Ile Ser Gly Gln Met Lys Gln Pro Leu Gln Ala Asn Met Pro Ser Ile 2210 2215 2220 Ser Arg Gly Arg Thr Met Ile His Ile Pro Gly Val Arg Asn Ser Ser 2225 2230 2235 2240 Ser Ser Thr Ser Pro Val Ser Lys Lys Gly Pro Pro Leu Lys Thr Pro 2245 2250 2255 Ala Ser Lys Ser Pro Ser Glu Gly Gln Thr Ala Thr Thr Ser Pro Arg 2260 2265 2270 Gly Ala Lys Pro Ser Val Lys Ser Glu Leu Ser Pro Val Ala Arg Gln 2275 2280 2285 Thr Ser Gln Ile Gly Gly Ser Ser Lys Ala Pro Ser Arg Ser Gly Ser 2290 2295 2300 Arg Asp Ser Thr Pro Ser Arg Pro Ala Gln Gln Pro Leu Ser Arg Pro 2305 2310 2315 2320 Ile Gln Ser Pro Gly Arg Asn Ser Ile Ser Pro Gly Arg Asn Gly Ile 2325 2330 2335 Ser Pro Pro Asn Lys Ile Ser Gln Leu Pro Arg Thr Ser Ser Pro Ser 2340 2345 2350 Thr Ala Ser Thr Lys Ser Ser Gly Ser Gly Lys Met Ser Tyr Thr Ser 2355 2360 2365 Pro Gly Arg Gln Met Ser Gln Gln Asn Leu Thr Lys Gln Thr Gly Leu 2370 2375 2380 Ser Lys Asn Ala Ser Ser Ile Pro Arg Ser Glu Ser Ala Ser Lys Gly 2385 2390 2395 2400 Leu Asn Gln Met Asn Asn Gly Asn Gly Ala Asn Lys Lys Val Glu Leu 2405 2410 2415 Ser Arg Met Ser Ser Thr Lys Ser Ser Gly Ser Glu Ser Asp Arg Ser 2420 2425 2430 Glu Arg Pro Val Leu Val Arg Gln Ser Thr Phe Ile Lys Glu Ala Pro 2435 2440 2445 Ser Pro Thr Leu Arg Arg Lys Leu Glu Glu Ser Ala Ser Phe Glu Ser 2450 2455 2460 Leu Ser Pro Ser Ser Arg Pro Ala Ser Pro Thr Arg Ser Gln Ala Gln 2465 2470 2475 2480 Thr Pro Val Leu Ser Pro Ser Leu Pro Asp Met Ser Leu Ser Thr His 2485 2490 2495 Ser Ser Val Gln Ala Gly Gly Trp Arg Lys Leu Pro Pro Asn Leu Ser 2500 2505 2510 Pro Thr Ile Glu Tyr Asn Asp Gly Arg Pro Ala Lys Arg His Asp Ile 2515 2520 2525 Ala Arg Ser His Ser Glu Ser Pro Ser Arg Leu Pro Ile Asn Arg Ser 2530 2535 2540 Gly Thr Trp Lys Arg Glu His Ser Lys His Ser Ser Ser Leu Pro Arg 2545 2550 2555 2560 Val Ser Thr Trp Arg Arg Thr Gly Ser Ser Ser Ser Ile Leu Ser Ala 2565 2570 2575 Ser Ser Glu Ser Ser Glu Lys Ala Lys Ser Glu Asp Glu Lys His Val 2580 2585 2590 Asn Ser Ile Ser Gly Thr Lys Gln Ser Lys Glu Asn Gln Val Ser Ala 2595 2600 2605 Lys Gly Thr Trp Arg Lys Ile Lys Glu Asn Glu Phe Ser Pro Thr Asn 2610 2615 2620 Ser Thr Ser Gln Thr Val Ser Ser Gly Ala Thr Asn Gly Ala Glu Ser 2625 2630 2635 2640 Lys Thr Leu Ile Tyr Gln Met Ala Pro Ala Val Ser Lys Thr Glu Asp 2645 2650 2655 Val Trp Val Arg Ile Glu Asp Cys Pro Ile Asn Asn Pro Arg Ser Gly 2660 2665 2670 Arg Ser Pro Thr Gly Asn Thr Pro Pro Val Ile Asp Ser Val Ser Glu 2675 2680 2685 Lys Ala Asn Pro Asn Ile Lys Asp Ser Lys Asp Asn Gln Ala Lys Gln 2690 2695 2700 Asn Val Gly Asn Gly Ser Val Pro Met Arg Thr Val Gly Leu Glu Asn 2705 2710 2715 2720 Arg Leu Asn Ser Phe Ile Gln Val Asp Ala Pro Asp Gln Lys Gly Thr 2725 2730 2735 Glu Ile Lys Pro Gly Gln Asn Asn Pro Val Pro Val Ser Glu Thr Asn 2740 2745 2750 Glu Ser Ser Ile Val Glu Arg Thr Pro Phe Ser Ser Ser Ser Ser Ser 2755 2760 2765 Lys His Ser Ser Pro Ser Gly Thr Val Ala Ala Arg Val Thr Pro Phe 2770 2775 2780 Asn Tyr Asn Pro Ser Pro Arg Lys Ser Ser Ala Asp Ser Thr Ser Ala 2785 2790 2795 2800 Arg Pro Ser Gln Ile Pro Thr Pro Val Asn Asn Asn Thr Lys Lys Arg 2805 2810 2815 Asp Ser Lys Thr Asp Ser Thr Glu Ser Ser Gly Thr Gln Ser Pro Lys 2820 2825 2830 Arg His Ser Gly Ser Tyr Leu Val Thr Ser Val 2835 2840 31 65 DNA Artificial Sequence Description of Artificial Sequencesourcesynthesized 31 cggaattcnn nnnnnnnaac agcnnnnnnn nnaatgaann ncaaagtctg nnntgaggat 60 cctca 65 32 65 DNA Artificial Sequence Description of Artificial Sequencesourcesynthesized 32 cggaattcga ctcagaannn nnnaacttca gannnnnnat cnnnnnnnnn gtctgaggat 60 cctca 65 33 65 DNA Artificial Sequence Description of Artificial Sequencesourcesynthesized 33 cggaattcnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnntgaggat 60 cctca 65 34 4 PRT Artificial Sequence Description of Artificial Sequencesourcemotif 34 Gly Leu Gly Phe 1

Claims (19)

1. A method of preparing a protein array based on biochemical protein-protein interaction, comprising the steps of:
(a) depositing on a substrate an array of a first protein, the first protein comprising a PDZ domain; and
(b) applying a second protein, which comprises an amino acid sequence (S/T)-X-(V/I/L)-COOH, to the first protein array, the amino acid sequence (S/T)-X-(V/I/L)-COOH of the second protein binding to the PDZ domain of the first protein,
wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternative to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group consisting of alanine, cysteine, aspartic acid, glutamic acid, phenylalanine, glycine, histidine, isoleucine, lysine, leucine, methionine, asparagine, proline, glutamine, arginine, serine, threonine, valine, tryptophan and tyrosine.
2. The method of claim 1, wherein the amino acid sequence (S/T)-x-(V/I/L) is fused to the C-terminal of the second protein.
3. The method of claim 1, wherein the protein array is maintained under physiological condition, and is used to screen one or more drug targets.
4. The method of claim 1, wherein the first protein deposited in step (a) is in a soluble buffer.
5. The method of claim 1, wherein the first protein deposited in step (a) is immobilized in a gel.
6. The method of claim 1, wherein the substrate includes a plurality of microwells contained therein, and the first protein is deposited in step (a) into the microwells.
7. The method of claim 1, wherein the substrate includes a glass plate, and the first protein array is printed onto the glass plate in step (a).
8. The method of claim 1, wherein the substrate includes a glass plate and a plurality of gel pads on the glass plate, and the first protein is deposited in step (a) onto the gel pads.
9. The method of claim 1, wherein the first protein is deposited on the substrate by a robot.
10. The method of claim 1, wherein at least one array element of the protein array includes an oligonucleotide.
11. The method of claim 1, wherein at least one array element of the protein array includes messenger RNA.
12. The method of claim 1, wherein at least one array element of the protein array includes DNA.
13. The method of claim 1, wherein at least one array element includes a sugar.
14-15 (canceled).
16. A method of preparing a protein polypeptide array, comprising the steps of:
(a) depositing on a substrate an array of a first polypeptide, the first polypeptide comprising a PDZ domain; and
(b) applying a second polypeptide which comprises an amino acid sequence (s/T)-X-(V/I/L)-COOH to the first polypeptide array, the amino acid sequence (S/T)-X-(V/I/L)—COOH of the second polypeptide binding to the PDZ domain of the first polypeptide,
wherein each hyphen represents a peptide bond, each parenthesis encloses amino acids which are alternatives to one other, each slash within such parentheses separates the alternative amino acids, and the X represents any amino acid which is selected from the group consisting of alanine, cysteine, aspartic acid, glutamic acid, phenylalanine, glycine, histidine, isoleucine, lysine, leucine, methionine, asparagine, praline, glutamine, arginine, serine, threonine, valine, tryptophan and tyrosine.
17. The method of claim 16, wherein at least one array element includes an oligonucleotide in addition to the first polypeptide.
18. The method of claim 16, wherein at least one array element includes messenger RNA in addition to the first polypeptide.
19. The method of claim 16, wherein at least one array element includes DNA in addition to the first polypeptide.
20. The method of claim 16, wherein at least one array element includes a sugar in addition to the first polypeptide.
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