Patent Publication Number: US-6214582-B1

Title: Y2H35 a strong IKK binding protein

Description:
BACKGROUND OF THE INVENTION 
     The NF-κB family of transcription factors are involved in the regulation of a wide variety of cellular responses. These transcription factors mediate extracellular signals that induce expression of genes involved in such diverse processes as cell division, inflammation, and apoptosis. See, for example, Baldwin, Annu. Rev. Immunol. 12, 141-179 (1996); Beg and Baltimore, Science 274, 782-274 (1996); Gilmore et al., Oncogene 13, 1267-1378 (1996); Mayo, et al, Science 278, 1812-1815 (1997); and Van Antwerp et al., Science 274, 787-789 (1996); Ashkenazi and Dixit, Science 281, 1305-1308 (1998). 
     NF-κB is anchored in the cytoplasm of most non-stimulated cells by a non-covalent interaction with one of several inhibitory proteins known as IκBs. See for example, Baeuerle and Baltimore, Science 242, 540-546 (1988). Cellular stimuli associated with immune and inflammatory responses, for example inflammatory cytokines such as tumor necrosis factor α (TNFα) or interleukin-1 (IL-1), activate kinases, which in turn activate NF-κB by phosphorylating IκBs. The kinases that phosphorylate IκBs are called IκB kinases (IKKs). 
     Phosphorylation marks the IκBs for ubiquitination and proteosome mediated degradation. The degradation and dissociation, of IκBs from NF-κB unmasks the NF-κB nuclear localization signal, and facilitates the nuclear translocation of active NF-κB to the nucleus, thereby upregulating NF-κB responsive target genes. See, for example, Baeuerle and Henkel, Annu. Rev. Immunol. 12, 141-179 (1994); Baldwin, Annu.Rev. Immunol. 14, 649-683 (1996); Siebenlist et al., Annu.Rev.Cell Biol. 12, 405-455 (1994); and Verma et al, Genes Dev. 9, 2723-2735 (1995). Thus, this phosphorylation of IκBs is a key regulatory step for NF-κB mediated processes. 
     The determination and characterization of kinases that directly phosphorylate IκBs are instrumental in the delineation of signaling pathways involving NF-κB activation. Recently, an IκB kinase, designated IKKα but also referred to as CHUK (conserved helix-loop-helix ubiquitous kinase), was identified in a yeast-two-hybrid screen with NIK as bait. Regnier et al., Cell 90, 373-383 (1997). IKKα was determined to be responsible for the major IκB kinase activity induced by TNF stimulation of HeLa cells. DiDonato et al., Nature 388, 548-554 (1997). The identification of IKKα as a cytoplasmic kinase which phosphorylates IκB family members at their physiologically relevant sites and targets them for proteosome-mediated degradation was a major breakthrough. 
     The IKKα gene encodes a 745 amino-acid polypeptide (having a molecular mass of approximately 85 kDa). Murine and human IKKα cDNA clones were found to be almost identical. Connelly and Marcu, Cellular and Molecular Biology Research 41, 537-549 (1995). 
     Another kinase, termed IKKβ, homologous to IKKα, has also been reported. Stancovski and Baltimore, Cell 91, 299-302 (1997); Woronicz et al., Science 278, 866-869 (1997); and Zandi et al., Cell 91, 243-252 (1997). IKKα and IKKβ have 52% overall similarity to each other and 65% identity in the kinase domain. Zandi et al., Cell 91, 243-252 (1997). An IκB kinase termed T2K has also been described in U.S. Pat. No. 5,776,717 to Cao. 
     The known IκB protein kinases generally phosphorylate IκBs at specific serine residues. For example, they specifically phosphorylate serines 32 and 36 of IκBα. Phosphorylation of both sites is required to efficiently target IκBα for destruction in vivo. Moreover, activation of IKKα and IKKβ occurs in response to NF-κB activating agents and mutant IKKα and IKKβ that are catalytically inactive block NF-κB stimulation by cytokines. These results highlight the important role played by IκB protein kinases in NF-κB activation processes. See Stancovski and Baltimore, Cell 91, 299-302 (1997) for a recent discussion of IκB kinases. 
     IKKα and IKKβ have structural motifs characteristic of the IKK kinases. This includes an amino terminal serine-threonine kinase domain separated from a carboxyl proximal helix-loop-helix (H-L-H) domain by a leucine zipper domain. These structural characteristics are unlike other kinases, and the domains are thought to be involved in protein-protein interactions. 
     Numerous proteins are involved in the signaling pathways that lead to immune, inflammatory, and apoptotic responses. A complete elucidation of these processes requires the identification of additional proteins that are involved and a determination of the protein interactions. 
     The discovery of additional proteins involved in these processes is important for controlling immune, apoptotic, and inflammatory processes. Thus, there is a great need for the identification and characterizion of additional proteins involved in IKK mediated cellular processes. 
     SUMMARY OF THE INVENTION 
     The present invention provides an isolated IKK binding protein, designated Y2H35, comprising the amino acid sequence set forth in SEQ ID NO:1 and functional equivalents. Also included are isolated nucleic acid molecules that encode Y2H35. Methods of making Y2H35 comprising expressing nucleic acid molecules encoding the protein are also provided. Antibodies directed to Y2H35 are also included in the invention. 
     DETAILED DESCRIPTION OF THE INVENTION 
     The invention is directed to an IKK binding protein, designated Y2H35, and its functional equivalents. Y2H35 will hereinafter refer to the protein defined by SEQ ID NO:1, which is found in humans. 
     In this specification, functional equivalents are proteins or fragments that are substantially homologous to SEQ ID NO:1 and that specifically bind to an IKK protein, such as IKKα or IKKβ. The term IKK is used herein to refer to all kinases that phosphorylate any IκB and that have helix-loop-helix and leucine zipper domains. Y2H35 and its functional equivalents bind to the region of the IKK proteins made up of the contiguous helix-loop-helix and leucine zipper domains. 
     In order to determine whether the sequence of a first protein, or fragment thereof, is substantially homologous to the sequence of a second protein, such as Y2H35, or fragment thereof, the sequences are first aligned so as to optimize the percent of amino acid residues that are identical, or that are identical or equivalent, at corresponding positions. Gaps may be introduced in the sequences, if necessary, to achieve optimization. 
     Amino acids generally considered to be equivalent are indicated below in separate rows (a) through (e): 
     (a) Ala (A), Ser (S), Thr (T), Pro (P), Gly (G) 
     (b) Asn (N), Asp (D), Glu (E), Gln (Q) 
     (c) His (H), Arg (R), Lys (K) 
     (d) Met (M), Leu (L), Ile (I), Val (V) 
     (e) Phe (F), Tyr (Y), Trp (W) 
     The amino acid sequences of highly homologous proteins can usually be aligned by visual inspection. If visual inspection is insufficient, the proteins are aligned in accordance with any of the methods described by George, D. G. et al, in  Macromolecular Sequencing and Synthesis, Selected Methods and Applications,  pages 127-149, Alan R. Liss, Inc. (1988), such as the formula described at page 137 using a match score of 1, a mismatch score of 0, and a gap penalty of −1. 
     In a first embodiment, the sequence of a protein or fragment thereof is considered substantially homologous to the sequence of Y2H35 or a fragment thereof if the amino acid sequences, after alignment, are at least about 25% identical, preferably at least about 35% identical, more preferably at least about 50% identical, even more preferably at least about 65% identical, still more preferably at least about 75% identical, most preferably at least about 85% identical, and, ideally at least about 95% identical. 
     In a second embodiment, the sequence of a protein or fragment thereof is considered substantially homologous to the sequence of Y2H35 or a fragment thereof if the amino acid sequences, after alignment, are at least about 50% identical or equivalent, preferably at least about 65% identical or equivalent, most preferably at least about 85% identical or equiavalent, and ideally at least about 95% identical or equivalent. 
     Functional equivalents include all modifications of the polypeptide set forth in SEQ ID NO:1. These modifications may be introduced deliberately, as by site-directed mutagenesis, or may be natural variations and mutations. Such modifications include substitutions, additions, and/or deletions in the protein sequences as long as substantial homology and specific binding to IKK proteins are maintained. 
     For example, functional equivalents include variant Y2H35 proteins that are expressed by naturally occurring alleles. Alleles are alternative forms of a gene that occupy a given locus of a chromosome within a species. 
     Functional equivalents of Y2H35 also include proteins from non-human mammalian species (species orthologs) as well as proteins expressed by alleles of such species orthologs. Non-human mammals include, for example, primates, pet animals such as dogs and cats, laboratory animals such as rats and mice, and farm animals such as horses, sheep, and cows. 
     The proteins of the invention that do not occur in nature are isolated. The term “isolated” as used herein, in the context of proteins, refers to a Y2H35 polypeptide which is unaccompanied by at least some of the material with which it is associated in its natural state. The isolated protein constitutes at least 0.5%, preferably at least 5%, more preferably at least 25% and still more preferably at least 50% by weight of the total protein in a given sample. 
     Most preferably the “isolated” protein is substantially free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated, and yields a single major band on a non-reducing polyacrylamide gel. Substantially free means that the protein is at least 75%, preferably at least 85%, more preferably at least 95% and most preferably at least 99% free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated. 
     The invention also provides novel and/or isolated nucleic acid molecules that encode SEQ ID NO:1 and the functional equivalents thereof. Nucleic acid molecules (nucleic acids) of the invention include deoxyribonucleic acid (DNA), complementary DNA (cDNA), and ribonucleic acid (RNA) sequences. 
     For example, the invention includes an isolated nucleic acid molecule as set forth in either SEQ ID NO:2 or SEQ ID NO:3, isolated nucleic acid molecules that are substantially homologous with SEQ ID NO:2 or SEQ ID NO:3, isolated nucleic acid molecules that hybridize with SEQ ID NO:2 or SEQ ID NO:3 under stringent conditions, nucleic acid sequences that are degenerate as a result of the genetic code, and the complements and fragments thereof. 
     In order to determine whether the sequence of a first nucleic acid molecule, or fragment thereof, is substantially homologous to the sequence of a second nucleic acid molecule, such as SEQ ID NO: 2, or fragment thereof, the sequences are first aligned so as to optimize the percent of nucleotides that are identical at corresponding positions. Gaps may be introduced in the sequences if necessary to achieve optimization. 
     The nucleic acid sequences of highly homologous nucleic acid molecules can usually be aligned by visual inspection. If visual inspection is insufficient, the nucleic acid molecules are aligned in accordance with any of the methods described by George, D. G. et al, in  Macromolecular Sequencing and Synthesis, Selected Methods and Applications,  pages 127-149, Alan R. Liss, Inc. (1988), such as the formula described at page 137 using a match score of 1, a mismatch score of 0, and a gap penalty of −1. 
     In the present specification, the sequence of a nucleic acid molecule or fragment thereof is considered substantially homologous to SEQ ID NO:2, or a fragment thereof, if the nucleic acid sequences, after alignment, are at least about 40% identical, preferably at least about 50% identical, more preferably at least about 60% identical, even more preferably at least about 70% identical, still more preferably at least about 80% identical, most preferably at least about 90% identical, and, ideally at least about 95% identical. 
     The invention also includes nucleic acid molecules that hybridize to SEQ ID NO:2 or SEQ ID NO:3, a fragment of SEQ ID NO:2, a complement of SEQ ID NO:2, or a complement of a fragment of SEQ ID NO:2 under stringent conditions. 
     Also included in the invention are a preferred group of protein functional equivalents of SEQ ID NO:1 encoded by nucleic acid molecules that hybridize under stringent conditions to a sequence complementary to SEQ ID NO:2 or a fragment of SEQ ID NO:2. 
     The term “stringent conditions,” as used herein, is equivalent to “high stringent conditions” and “high stringency.” These terms are used interchangeably in the art. 
     Stringent conditions are defined in a number of ways. In one definition, stringent conditions are selected to be about 50° C. lower than the thermal melting point (T m ) for a specific sequence at a defined ionic strength and pH. The T m  is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched sequence. Typical stringent conditions are those in which the salt concentration is about 0.02 M at pH 7 and the temperature is at least about 60° C. Further examples of stringent conditions can be found in U.S. Pat. No. 5,789,550 to Goeddel et al. (1998). The description of stringent conditions in U.S. Pat. No. 5,789,550 is herein incorporated by reference. 
     Stringent conditions, in the nucleic acid hybridization context, include a combination of conditions, such as the nature and concentration of salts and organic solvents, temperature, and other parameters that are typically known to control hybridization reactions. The combination of parameters is more important than the measure of any single parameter. See U.S. Pat. No. 5,786,210; Wetmur and Davidson, J. Mol. Biol. 31, 349-370 (1968). Generally, stringent conditions are obtained at higher temperatures and lower ionic strength. Control of hybridization conditions, and the relationships between hybridization conditions and degree of homology are understood by those skilled in the art. See, for example, Bej, A. K., Nucleic Acid Hybridizations: Principles and Strategies, in Dangler, C. A. ed,  Nucleic Acid Analysis: Principles and Bioapplications,  Wiley-Liss, Inc., pp. 1-29 (1996); Adams et al.,  The Biochemistry of the Nucleic Acids,  pp. 605-606, Chapman &amp; Hall (1992); Sambrook J, Fritsch E F, and Maniatis T,  Molecular Cloning, A Laboratory Manual,  2d ed., Cold Spring Harbor Laboratory, Cold Spring Harbor (1989). 
     Fragments of nucleic acid molecules of the invention include primers and probes which are useful as tools in molecular biology and biotechnology. The fragment may or may not encode a polypeptide that binds to IKKα or IKKβ. Even if the encoded polypeptide does not bind, the fragment can be used, for example, as a primer (“amplimer”) to selectively amplify nucleic acid, such as genomic DNA or total RNA. Primers can also be used in nucleic acid amplification procedures such as the polymerase chain reaction (PCR), ligase chain reaction (LCR), repair chain reaction (RCR), PCR oligonucleotide ligation assay (PCR-OLA), and the like. 
     Fragments of the nucleic acid molecules of the invention can also be oligonucleotides complementary to a target nucleic acid molecule, i.e., the fragment can be a probe. Such oligonucleotides can be DNA or RNA. Oligonucleotides useful as probes in hybridization studies, such as in situ hybridization, can also be constructed. 
     The length of the oligonucleotide probe is not critical, as long as it is capable of hybridizing to the target molecule. The oligonucleotide should contain at least 6 nucleotides, preferably at least 10 nucleotides, and more preferably, at least 15 nucleotides. There is no upper limit to the length of the oligonucleotide probes. Longer probes are more difficult to prepare and require longer hybridization times. Therefore, the probe should not be longer than necessary. Normally, the oligonucleotide probe will not contain more than 50 nucleotides, preferably not more than 40 nucleotides, and, more preferably, not more than 30 nucleotides. 
     Numerous methods for detectably labeling such probes with radioisotopes, fluorescent tags, enzymes, binding moieties (e.g., biotin), and the like are known, so that the probes of the invention can be adapted for easy detectability. Methods for making and using nucleic acid probes are understood by those skilled in the art. See, for example, Keller G H and Manak M M,  DNA Probes,  2d ed., Macmillan Publishers Ltd., England (1991) and Hames B D and Higgins S J, eds.,  Gene Probes I  and  Gene Probes II,  IRL Press, Oxford (1995). 
     The nucleic acid molecules may contain synthetic sequences that do not occur in nature and/or they are isolated. The term “isolated,” as used herein, in the context of nucleic acids, includes nucleic acid molecules unaccompanied by at least some of the material with which they are associated in their natural state. The isolated nucleic acid may constitute at least 0.5%, preferably at least 5%, more preferably at least 25% and still more preferably at least 50% by weight of the total nucleic acid in a given sample. Most preferably the “isolated” nucleic acid is substantially free of other nucleic acids, proteins, lipids, carbohydrates or other materials with which it is naturally associated. Substantially free means that the nucleic acid is at least 75%, preferably at least 85%, more preferably at least 95% and most preferably at least 99% free of other nucleic acids, proteins, lipids, carbohydrates or other materials with which it is naturally associated. The nucleic acid molecules of the invention can also be recombinant, meaning that they comprise a non-natural sequence or a natural sequence joined to nucleotide(s) other than than those in which they are joined on the natural chromosome. 
     Y2H35 was shown, using yeast two-hybrid screens, to bind to the carboxyl terminal domain regions of IKKα and IKKβ. See example 1. Y2H35 specifically binds with the region of the IKK proteins made up of the contiguous helix-loop-helix and leucine zipper domains. The binding of the Y2H35 protein to the IKKs is stronger than the binding of IKKα to a natural substrate of IKKα, viz. IκBβ2. 
     The Y2H35 protein and the other IKKα binding proteins described in example 1 are useful for elucidating and controlling pathways leading to inflammation and apoptosis. These processes are mediated by receptors such as tumor necrosis factor (TNF) receptors. The IKK binding proteins can also be used to detect IKK complexes and modulate IKK activity in cells undergoing signalling by inflammatory mediators such as TNFα and Il-1. 
     The Y2H35 proteins are also useful for identifying therapeutically active agents that modulate the binding or interaction of Y2H35 and either IKKα or IKKβ. Such compounds can either prevent the formation of Y2H35/IKK complexes or prevent or inhibit the dissociation of Y2H35/IKK complexes. Molecules that prevent the formation of Y2H35/IKK complexes or inhibit the dissociation of these complexes are useful for boosting the immune system, or as immunosuppresants, or as antiinflammatory agents. 
     Complex formation or dissociation can be determined by methods well known in the art. Such methods include, for example, gel filtration, sucrose density gradient centrifugation, crosslinking, and immunoprecipitation. 
     The proteins and variants of the proteins can be prepared by methods known in the art. Such methods include isolating the protein directly from cells, and synthesizing the protein chemically from individual amino acids. Preferably, the proteins of the invention can be prepared by providing DNA that encodes the protein, amplifying or cloning the DNA, expressing the DNA in a suitable host, and harvesting the protein. 
     DNA encoding the proteins of the invention can be synthesized or isolated. The DNA of the invention can be synthesized chemically from the four nucleotides in whole or in part by methods known in the art. Such methods include those described by Caruthers, Science 230, 281-285 (1985). DNA can also be synthesized by preparing overlapping double-stranded oligonucleotides, filling in the gaps, and ligating the ends together. See, generally, Sambrook et al. (1989) and Glover D M and Hames B D, eds.,  DNA Cloning,  2d ed., Vols. 1-4, IRL Press, Oxford (1995). 
     DNA expressing functional homologs of the protein can be prepared from wild-type DNA by site-directed mutagenesis. See, for example, Zoller and Smith, Nucleic Acids Res 10, 6487-6500 (1982); Zoller, Methods Enzymol 100, 468-500 (1983); Zoller, DNA 3(6), 479-488 (1984); and McPherson, ed.,  Directed Mutagenesis: A Practical Approach,  IRL Press, Oxford (1991). 
     DNA encoding the protein of the invention can be isolated from different species by using the human sequence, SEQ ID NO:2, to prepare one or more oligonucleotide probes. The probe is labeled and used to screen a genomic or cDNA library in a suitable vector, such as phage lambda. The homology between the DNA of the Y2H35 of the species being screened and that of the human DNA is taken into account in determining the conditions of hybridization. The cDNA library may be prepared from mRNA by known methods, such as those described in Gubler and Hoffman, Gene 25, 263-270 (1983). Oligonucleotide probes can be used to screen cDNA libraries from different species and tissues. The oligonucleotide probe should be labeled so that it can be detected upon hybridization to DNA in the library being screened. These methods are well known in the art. 
     The DNA isolated is sequenced, and the sequence used to prepare additional oligonucleotide probes. This procedure may be repeated to obtain overlapping fragments until a complete open reading frame is produced. 
     The nucleic acids of the invention may be amplified by methods known in the art. One suitable method is the polymerase chain reaction (PCR) method described by Saiki et al., Science 239, 487 (1988), Mullis et al in U.S. Pat. No. 4,683,195 and by Sambrook et al. (1989). It is convenient to amplify the clones in the lambda-gt10 or lambda-gt11 vectors using lambda-gt10 or lambda-gt11-specific oligomers as the amplimers (available from Clontech, Palo Alto, Calif.). Other amplification procedures that are well known in the art such as ligase chain reaction (LCR), repair chain reaction (RCR), and PCR oligonucleotide ligation assay (PCR-OLA) can also be used to amplify the nucleic acids of the invention. 
     DNA encoding the proteins of the invention, or unique fragments thereof, may also be cloned in a suitable host cell and expressed by methods well known in the art. The DNA and protein may be recovered from the host cell. See, generally, Sambrook et al. (1989), for methods relating to the manufacture and manipulation of nucleic acids. The entire gene or additional fragments of the gene can be isolated by using the known DNA sequence or a fragment thereof as a probe. To do so, restriction fragments from a genomic or cDNA library may be identified by Southern hybridization using labeled oligonucleotide probes derived from SEQ ID NO:2. 
     The amplified or cloned DNA can be expressed in a suitable expression vector by methods known in the art. See, generally, Sambrook et al. (1989). 
     A variety of expression vectors and host cell systems can be used. These include, for example, microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA, or cosmid DNA containing the Y2H35 coding region. Other expression vectors and host cell systems that can be used include yeast transformed with recombinant yeast expression vectors containing the Y2H35 coding sequence, insect cells infected with recombinant virus expression vectors containing the Y2H35 coding sequence, plant cells infected with recombinant virus expression vectors containing the Y2H35 coding sequence, or animal cells infected with recombinant virus expression vectors (e.g., retroviruses, adenovirus, vaccinia virus) containing the Y2H35 coding sequence. 
     The expression vectors useful in the present invention contain at least one expression control sequence that is operatively linked to the DNA sequence or fragment to be expressed. The control sequence is inserted in the vector in order to control and to regulate the expression of the cloned DNA sequence. Examples of useful expression control sequences are the lac system, the trp system, the tac system, the trc system, major operator and promoter regions of phage lambda, the control region of fd coat protein, the glycolytic promoters of yeast, e.g., the promoter for 3-phosphoglycerate kinase, the promoters of yeast acid phosphatase, e.g., Pho5, the promoters of the yeast alpha-mating factors, and promoters derived from polyoma, adenovirus, retrovirus, and simian virus, e.g., the early and late promoters or SV40, and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells and their viruses or combinations thereof. 
     Useful expression hosts include well-known prokaryotic and eukaryotic cells. Some suitable prokaryotic hosts include, for example,  E. coli,  such as  E. coli  SG-936,  E. coli  HB 101,  E. coli  W3110,  E. coli  X1776,  E. coli  X2282,  E. coli  DHI, and  E. coli  MRC1, Pseudomonas sp., Bacillus sp., such as  B. subtilis,  and Streptomyces sp. Suitable eukaryotic cells include yeasts and other fungi, insect, animal cells, such as COS cells and CHO cells, human cells and plant cells in tissue culture. 
     Preferably, Y2H35 is expressed using baculoviral vectors in insect cell cultures. In general, the transformation of insect cells and production of foreign proteins therein is disclosed in Guarino et al., U.S. Pat. No. 5,162,222. 
     Proteins can be isolated from a solubilized fraction by standard methods. Some suitable methods include precipitation and liquid chromatographic protocols such as ion exchange, hydrophobic interaction, and gel filtration. See, for example,  Methods Enzymol  ( Guide to Protein Chemistry,  Deutscher, ed., Section VII) pp. 182:309 (1990) and Scopes,  Protein Puirification,  Springer-Verlag, N.Y. (1987), which are herein incorporated by reference. 
     Alternatively, purified material is obtained by separating the protein on preparative SDS-PAGE gels, slicing out the band of interest and electroeluting the protein from the polyacrylamide matrix by methods known in the art. The detergent SDS is removed from the protein by known methods, such as by dialysis or the use of a suitable column, such as the Extracti-Gel column from Pierce. Mixtures of proteins can be separated by, for example, SDS-PAGE in accordance with the method of Laemmli, Nature 227, 680-685 (1970). Such methods are well known in the art. 
     The proteins of the invention can also be chemically synthesized by methods known in the art. Suitable methods for synthesizing proteins are described by Stuart and Young,  Solid Phase Peptide Synthesis,  2d ed., Pierce Chemical Company (1984). 
     The invention also includes an antibodies or antibody fragments that specifically bind to epitopes of the proteins of the invention defined by the amino acid sequence set forth in SEQ ID NO:1. An “antibody” in accordance with the present specification is defined broadly as a protein that binds specifically to an epitope. The antibodies of the invention can be monoclonal antibodies, polyclonal antibodies, chimerized antibodies, humanized antibodies, single chain antibodies, or a fragment thereof. For use in in vivo applications with human subjects, the antibody is preferably chimerized or humanized, containing an antigen binding region from, e.g., a rodent, with the bulk of the antibody replaced with sequences derived from human immunoglobulin. 
     Antibodies further include recombinant polyclonal or monoclonal Fab fragments prepared in accordance with the method of Huse et al., Science 246,1275-1281 (1989). 
     Polyclonal antibodies are isolated from mammals that have been inoculated with the protein or a functional analog in accordance with methods known in the art. Briefly, polyclonal antibodies may be produced by injecting a host mammal, such as a rabbit, mouse, rat, or goat, with the protein or a fragment thereof capable of producing antibodies that distinguish between mutant and wild-type protein. The peptide or peptide fragment injected may contain the wild-type sequence or the mutant sequence. Sera from the mammal are extracted and screened to obtain polyclonal antibodies that are specific to the peptide or peptide fragment. 
     The antibodies are preferably monoclonal. Monoclonal antibodies may be produced by methods known in the art. These methods include the immunological method described by Kohler and Milstein, Nature 256:495-497 (1975) and by Campbell, in Burdon et al., eds,  Laboratory Techniqnies in Biochemistry and Molecular Biology,  Vol. 13, Elsevier Science Publishers, Amsterdam (1985); as well as the recombinant DNA method described by Huse et al. (1989). 
     To produce monoclonal antibodies, a host mammal is inoculated with a peptide or peptide fragment as described above, and then boosted. Spleens are collected from inoculated mammals a few days after the final boost. Cell suspensions from the spleens are fused with a tumor cell in accordance with the general method described by Kohler and Milstein (1975). See also Campbell (1985). To be useful, a peptide fragment must contain sufficient amino acid residues to define the epitope of the molecule being detected. 
     If the fragment is too short to be immunogenic, it may be conjugated to a carrier molecule. Some suitable carrier molecules include keyhole limpet hemocyanin and bovine serum albumin. Conjugation may be carried out by methods known in the art. One such method is to combine a cysteine residue of the fragment with a cysteine residue on the carrier molecule. 
     Methods for making chimeric and humanized antibodies are also known in the art. For example, antibodies can be engineered using genetic techniques to produce chimeric antibodies including protein components from two or more species. 
     For example, methods for making chimeric antibodies include those described in U.S. patents by Boss (Celltech) and by Cabilly (Genentech). See U.S. Pat. Nos. 4,816,397 and 4,816,567, respectively. Methods for making humanized antibodies are described, for example, in Winter, U.S. Pat. No. 5,225,539, Co et al., Nature 351, 501-502 (1992); Queen et al., Proc. Natl. Acad. Sci. 86, 10029-1003 (1989) and Rodrigues et al., Int. J. Cancer, Supplement 7, 45-50 (1992). 
     Methods are also known for inducing expression of engineered antibodies in various cell types, such as mammalian and microbial cell types. Numerous techniques for preparing engineered antibodies are described, for example, in Owens and Young, “The genetic engineering of monoclonal antibodies,” J. Immunol. Meth. 168,149-165 (1994). 
     Methods for making single chain antibodies are also known in the art. Some suitable examples include those described by Wels et al. in European patent application 502 812 and Int. J. Cancer 60, 137-144 (1995). 
     Assays for directly detecting the presence of Y2H35 with antibodies follow known formats, such as, fluorescent activated flow cytometry, fluorescent microscopy, and immuno-electron microscopy. Moreover, assays for detecting the presence of proteins with antibodies have been previously described and follow known formats, such as standard blot and ELISA formats. These formats are normally based on incubating an antibody with a sample suspected of containing the protein and detecting the presence of a complex between the antibody and the protein. The antibody is labeled either before, during, or after the incubation step. The protein is preferably immobilized prior to detection. Immobilization may be accomplished by directly binding the protein to a solid surface, such as a microtiter well, or by binding the protein to immobilized antibodies. 
     Suitable assays are known in the art, such as the standard ELISA protocol described by R. H. Kenneth, “Enzyme-linked antibody assay with cells attached to polyvinyl chloride plates” in Kenneth et al.,  Monoclonal Antibodies,  Plenum Press, New York, pp. 376 et seq. (1981). 
    
    
     EXAMPLES 
     Example 1 
     Y2H35 Binds IKKα 
     A yeast two hybrid screen was undertaken with IKKα as a bait in an attempt to identify interacting proteins which could represent in vivo regulators of the cytokine induced kinase cascade. Full length IKKα and smaller fragments in the Field&#39;s pGTB9c bait vector (see Fields and Sternglanz, Trends Genet. 10, 286-292 (1994)) met with technical problems owing to its inherent in vivo transactivation properties. These problems were overcome by incorporating a high dose of an inhibitor of the product of the His3 selection gene thereby severely restricting yeast colony growth. (Triazole or 3-AT (3-amino-1, 2, 4-triazole or aminotriazole) has been reported to competitively inhibit the product of the yeast His3 gene in a dose dependent manner (Klopotowski et al., Arch. Biochem. Biophys. 112, 562-566 (1965)). The bait vector&#39;s insert was a 937 bp SnaB1/XhoI fragment of the murine IKKα clone encoding the protein&#39;s leucine zipper, helix-loop-helix and carboxyl terminus. The latter bait vector was transfected into the Y153 yeast strain and a colony that grew on agar without tryptophan was selected for further transfections according to standard protocols (Yeast Matchmaker manual, Clontech Inc., Palo Alto, Calif.). Yeast harboring the bait grew on histidine-minus plates. However, this non-specific growth was abrogated by the inclusion of 50 μM (3-AT) that would also yield the strongest interactors. Y153 cells harboring the bait vector were transfected with a B lymphoblast cDNA library (0.6×10 9  cfu, ATCC #87003) (Durfee et al., Genes Dev 7, 555-569 (1993)) sub-cloned into plasmid BNN132 (for a final transfection frequency of 10 5  clones), which were spread onto 30 agar plates (His-, Trp-, Leu-, 50 mM 3-AT). 126 clones showing a faster growth rate compared to background colonies were picked after 3 and 6 days incubtion at 30° C. and replated. 70 clones were selected for plasmid isolation based on their growth on His-, Trp-, Leu-, 50 μM 3-AT plates. From these 70 picks secondary picks, 16 clones remained positive after multiple rounds of purification and rescreening (14 of these sixteen were unique and two were isolated twice). 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Results of a Yeast Two-Hybrid Screen with IKKα Helix-Loop-Helix 
               
               
                 and Leucine Zipper Domains as Bait 
               
            
           
           
               
               
               
               
            
               
                   
                 Relative Interaction 
                 Insert 
                   
               
               
                 Y2h Clones 
                 Strength 
                 Length 
                 Identity 
               
               
                   
               
               
                 11 
                 + 
                 0.8 kB 
                 RanBP5 
               
               
                 52# 
                 ++ 
                 0.9 kB 
                 CoA Reductase 
               
               
                 21 
                 ++ 
                 1.3 kB 
                 TRIP9/HuIκBβ2 
               
               
                 29# 
                 ++ 
                 1.1 kB 
                 HuTCP-1 
               
               
                 31 
                 ++ 
                 1.5 kB 
                 Hsp40 
               
               
                 37 
                 + 
                 2.3 kB 
                 BS4 (Interferon 
               
               
                   
                   
                   
                 Induced Protein) 
               
               
                 67 
                 + 
                 1.5 kB 
                 Phospholipase A2 
               
               
                 71 
                 + 
                 0.8 kB 
                 Calmodulin 
               
               
                 70 
                 + 
                 1.5 kB 
                 HuSgn3 
               
               
                 14* 
                 ++ 
                 1.2 kB 
                 HuAD3 Locus 
               
               
                 35* 
                 +++ 
                 1.2 kB 
                 Cosmid near Btk 
               
               
                 56* 
                 +++ 
                 0.9 kB 
                 p33ING1-like 
               
               
                 53* 
                 +++ 
                 1.2 kB 
                 Unknown 
               
               
                 61** 
                 + 
                 0.7 kB 
                 Unknown 
               
               
                   
               
               
                 Legend: Fourteen yeast two hybrid clones obtained from a human B lymphoblastoid cell cDNA library which specifically interact with the contiguous helix-loop-belix and leucine zipper domains of the IKKα protein. Most clones (Y2h11,21,29, 70,14,35,56 and 53) also bound to an analogous IκKβ bait with similar or even greater strength except for Hsp40 which only specifically bound to the IκKα bait. All clones reproducibly failed to significantly interact with an empty bait vector and  
               
               
                 # two other bait vectors harboring either the IKKα Leucine Zipper or Helix-Loop-Helix domains. The relative interaction strengths are based on the growth rates (i.e., colony size) of each clone. #Isolated Twice; *Unknown strong interacting proteins; **Unknown weak interacting protein.  
               
            
           
         
       
     
     The fourteen clones are shown in Table 1. These results demonstrate the presence of a family of IKKα binding proteins. Nine of the 14 clones are known proteins and the remaining five specify novel proteins: three of which interact with the bait more strongly than IKKα&#39;s IκBβ substrate (Y2h35, 53 and 56), one in a comparable fashion to IκB (Y2h14) and one exhibited weaker binding (Y2h61). Several of the known proteins are involved in either signaling and/or molecular trafficking pathways in cells. RanBP5 was isolated as a Ran binding protein and Ran is a small GTP-binding and- hydrolyzing protein predominantly located in the nucleus (Deane et al., Mol. Cell Biol. 17, 5087-5096 (1998). RanBP5 is related to importin-β, a mediator of nuclear localization signal (NLS)-dependent nuclear transport. TRIP9/HulκBβ2 is the predominant isoform of IκBβ in human cells and a known physiological substrate of the IKKα kinase (Lee et al., Mol. Endocrinol. 9, 243-254 (1995); Hirano et al., Mol. Cell. Biol. 18, 2596-2607 (1998)). The presence of IκKβ amongst these IKKα interacting proteins validates the specificity of the screen and also demonstrates the IκBs do not require the IKKα amino terminal kinase domain for binding. Hsp40 and TCP-1 are chaperone proteins which might bind to the bait due to a partially unfolded conformation (in the context of a Ga14dbd chimera). A database of frequently isolated clones in yeast two hybrid screens does contain several hsp proteins but Hsp40 and TCP1 are not represented amongst these frequently isolated, presumably false positive genes. Alternatively, they may also be natural interactors of IKKα that might be involved in its in vivo cytoplasmic trafficking. HuSgn3 was recently described as a component of a 450 kDa protein complex that also possesses an IκB kinase activity. Seeger et al., FASEB J. 12, 469-478 (1998). Sgn3 also exhibited sequence similarities to regulatory components of the 26S proteasome complex. Calmodulin is the principal calcium sensor in the cell, which when complexed to two calcium ions, acts as a regulator for a variety of intracellular enzymes including kinases such as CaM-kinase II, the serine/threonine specific phosphatase, Calcineurin and proteins which maintain the cytoskeletal architecture. 
     Y2H35 is encoded by a novel transcript expressed within the AD3 and Btk (Bruton&#39;s tyrosine kinase) loci which have been respectively associated with early onset Alzheimer&#39;s disease (Sherrington et al., Nature 375, 754-760 (1995) and α-gamma-globulinemia (Kershaw and Dodsworth, Direct database submission of the nucleotide sequence of human cosmid V389H8, 1997). 
     
       
         
           
             3 
           
           
             1 
             379 
             PRT 
             Homo sapiens 
           
            1
Met Gly Tyr Ala Arg Lys Val Gly Trp Val Thr Ala Gly Leu Val Ile
  1               5                  10                  15
Gly Ala Gly Ala Cys Tyr Cys Ile Tyr Arg Leu Thr Arg Gly Arg Lys
             20                  25                  30
Gln Asn Lys Glu Lys Met Ala Glu Gly Gly Ser Gly Asp Val Asp Asp
         35                  40                  45
Ala Gly Asp Cys Ser Gly Ala Arg Tyr Asn Asp Trp Ser Asp Asp Asp
     50                  55                  60
Asp Asp Ser Asn Glu Ser Lys Ser Ile Val Trp Tyr Pro Pro Trp Ala
 65                  70                  75                  80
Arg Ile Gly Thr Glu Ala Gly Thr Arg Ala Arg Ala Arg Ala Arg Ala
                 85                  90                  95
Arg Ala Thr Arg Ala Arg Arg Ala Val Gln Lys Arg Ala Ser Pro Asn
            100                 105                 110
Ser Asp Asp Thr Val Leu Ser Pro Gln Glu Leu Gln Lys Val Leu Cys
        115                 120                 125
Leu Val Glu Met Ser Glu Lys Pro Tyr Ile Leu Glu Ala Ala Leu Ile
    130                 135                 140
Ala Leu Gly Asn Asn Ala Ala Tyr Ala Phe Asn Arg Asp Ile Ile Arg
145                 150                 155                 160
Asp Leu Gly Gly Leu Pro Ile Val Ala Lys Ile Leu Asn Thr Arg Asp
                165                 170                 175
Pro Ile Val Lys Glu Lys Ala Leu Ile Val Leu Asn Asn Leu Ser Val
            180                 185                 190
Asn Ala Glu Asn Gln Arg Arg Leu Lys Val Tyr Met Asn Gln Val Cys
        195                 200                 205
Asp Asp Thr Ile Thr Ser Arg Leu Asn Ser Ser Val Gln Leu Ala Gly
    210                 215                 220
Leu Arg Leu Leu Thr Asn Met Thr Val Thr Asn Glu Tyr Gln His Met
225                 230                 235                 240
Leu Ala Asn Ser Ile Ser Asp Phe Phe Arg Leu Phe Ser Ala Gly Asn
                245                 250                 255
Glu Glu Thr Lys Leu Gln Val Leu Lys Leu Leu Leu Asn Leu Ala Glu
            260                 265                 270
Asn Pro Ala Met Thr Arg Glu Leu Leu Arg Ala Gln Val Pro Ser Ser
        275                 280                 285
Leu Gly Ser Leu Phe Asn Lys Lys Glu Asn Lys Glu Val Ile Leu Lys
    290                 295                 300
Leu Leu Val Ile Phe Glu Asn Ile Asn Asp Asn Phe Lys Trp Glu Glu
305                 310                 315                 320
Asn Glu Pro Thr Gln Asn Gln Phe Gly Glu Gly Ser Leu Phe Phe Phe
                325                 330                 335
Leu Lys Glu Phe Gln Val Cys Ala Asp Lys Val Leu Gly Ile Glu Ser
            340                 345                 350
His His Asp Phe Leu Val Lys Val Lys Val Gly Lys Phe Met Ala Lys
        355                 360                 365
Leu Ala Glu His Met Phe Pro Lys Ser Gln Glu
    370                 375 
           
             2 
             1158 
             DNA 
             Homo sapiens 
           
            2
tctattgtcg gggacgattg catgggctac gccaggaaag taggctgggt gaccgcaggc     60
ctggtgattg gggctggcgc ctgctattgc atttatagac tgactagggg aagaaaacag    120
aacaaggaaa aaatggctga gggtggatct ggggatgtgg atgatgctgg ggactgttct    180
ggggccaggt ataatgactg gtctgatgat gatgatgaca gcaatgagag caagagtata    240
gtatggtacc caccttgggc tcggattggg actgaagctg gaaccagagc tagggccagg    300
gcaagggcca gggctacccg ggcacgtcgg gctgtccaga aacgggcttc ccccaattca    360
gatgataccg ttttgtcccc tcaagagcta caaaaggttc tttgcttggt tgagatgtct    420
gaaaagcctt atattcttga agcagcttta attgctctgg gtaacaatgc tgcttatgca    480
tttaacagag atattattcg tgatctgggt ggtctcccaa ttgtcgcaaa gattctcaat    540
actcgggatc ccatagttaa ggaaaaggct ttaattgtcc tgaataactt gagtgtgaat    600
gctgaaaatc agcgcaggct taaagtatac atgaatcaag tgtgtgatga cacaatcact    660
tctcgcttga actcatctgt gcagcttgct ggactgagat tgcttacaaa tatgactgtt    720
actaatgagt atcagcacat gcttgctaat tccatttctg acttttttcg tttattttca    780
gcgggaaatg aagaaaccaa acttcaggtt ctgaaactcc ttttgaattt ggctgaaaat    840
ccagccatga ctagggaact gctcagggcc caagtaccat cttcactggg ctccctcttt    900
aataagaagg agaacaaaga agttattctt aaacttctgg tcatatttga gaacataaat    960
gataatttca aatgggaaga aaatgaacct actcagaatc aattcggtga aggttcactt   1020
tttttctttt taaaagaatt tcaagtgtgt gctgataagg ttctgggaat agaaagtcac   1080
catgattttt tggtgaaagt aaaagttgga aaattcatgg ccaaacttgc tgaacatatg   1140
ttcccaaaga gccaggaa                                                 1158 
           
             3 
             1137 
             DNA 
             Homo sapiens 
           
            3
atgggctacg ccaggaaagt aggctgggtg accgcaggcc tggtgattgg ggctggcgcc     60
tgctattgca tttatagact gactagggga agaaaacaga acaaggaaaa aatggctgag    120
ggtggatctg gggatgtgga tgatgctggg gactgttctg gggccaggta taatgactgg    180
tctgatgatg atgatgacag caatgagagc aagagtatag tatggtaccc accttgggct    240
cggattggga ctgaagctgg aaccagagct agggccaggg caagggccag ggctacccgg    300
gcacgtcggg ctgtccagaa acgggcttcc cccaattcag atgataccgt tttgtcccct    360
caagagctac aaaaggttct ttgcttggtt gagatgtctg aaaagcctta tattcttgaa    420
gcagctttaa ttgctctggg taacaatgct gcttatgcat ttaacagaga tattattcgt    480
gatctgggtg gtctcccaat tgtcgcaaag attctcaata ctcgggatcc catagttaag    540
gaaaaggctt taattgtcct gaataacttg agtgtgaatg ctgaaaatca gcgcaggctt    600
aaagtataca tgaatcaagt gtgtgatgac acaatcactt ctcgcttgaa ctcatctgtg    660
cagcttgctg gactgagatt gcttacaaat atgactgtta ctaatgagta tcagcacatg    720
cttgctaatt ccatttctga cttttttcgt ttattttcag cgggaaatga agaaaccaaa    780
cttcaggttc tgaaactcct tttgaatttg gctgaaaatc cagccatgac tagggaactg    840
ctcagggccc aagtaccatc ttcactgggc tccctcttta ataagaagga gaacaaagaa    900
gttattctta aacttctggt catatttgag aacataaatg ataatttcaa atgggaagaa    960
aatgaaccta ctcagaatca attcggtgaa ggttcacttt ttttcttttt aaaagaattt   1020
caagtgtgtg ctgataaggt tctgggaata gaaagtcacc atgatttttt ggtgaaagta   1080
aaagttggaa aattcatggc caaacttgct gaacatatgt tcccaaagag ccaggaa      1137