Note: Descriptions are shown in the official language in which they were submitted.
WO 97/02347 ~ PCTtUS96/11170
A HUMAN MAP KINASE HOMOLOG
TECHNICAL FIELD
The present invention is in the field of molecular biology; more particularly, the
present invention describes a nucleic acid sequence and an amino acid sequence for a novel
human MAP kinase homolog.
,,
BACKGROUND ART
Mitogen-Activated Protein (MAP) Kinases
Mitogen-activated protein (MAP) kinases are a family of enzymes which regulate
0 intracellular signaling pathways. MAP kinases are important mediators of signal transduction
from cell surfaces to nuclei via phosphorylation c~c~des. Several subgroups of MAP kinases
have been defined and each manifests different substrate specificities and responds to various
distinct extracellular stimuli. Thus, the MAP kinase signaling pathways represent common
mechanisms for signal transduction by which different extracellular stimuli generate distinct
physiological responses inside cells (Egan SE and Weinberg RA (1993) Nature 365:781-
783) .
Various MAP kinase signaling pathways have been defined in ",al"i"alian cells as well as
in yeast. In mammalian cells, the extracellular stimuli activating the MAP kinase signaling
pathways include epidermal growth factor (EGF), ultraviolet light, hyperosmolar medium, heat
shock, endotoxic lipopolysaccharide (LPS), and pro-il,~lal"",atory cytokines such as tumor
necrosis factor (TNF) and interleukin-1 (IL-1). In the yeast, Saccharomyces cerevisiae.
various MAP kinase signaling pathways are activated by exposure to mating pheromone or
hyperosmolar environments and during cell-wall construction, sporulation and mitosis.
There are at least three subgroups of MAP kinases in mammalian cells (Derijard B et al
(1995) Science 267:682-5), and each subgroup is distinguished by a tripeptide sequence
motif. They are extracellular signal-regulated protein kinase (ERK) characterized by Thr-
Glu-Tyr, c-Jun amino-terminal kinase (JNK) characterized by Thr-Pro-Tyr, and p38 kinase
characterized by Thr-Gly-Tyr. The subgroups are activated by the dual phosphorylation of the
threonine and tyrosine by MAP kinase kinases located upstream of the phosphorylation casc~de.
Activated MAP kinases phosphorylate other effectors downstream ultimately leading to changes
inside the cell.
MAP Kinase Subgroup ERK
The ERK signal transduction pathway is activated via tyrosine kinase receptors on the
plasma membrane of the cell. When EGF or other growth factors bind to the tyrosine receptors,
they, in turn, bind to noncatalytic, src homology (SH) adaptor proteins (SH2-SH3-SH2) and a
~2~ ~7~9
WO 97/02347 PCT/US96/11170
guanine nucleotide releasing protein. The latter reduces GTP and activates Ras proteins,
members of the large family of guanine nucleotide binding proteins (G-proteins). The activated
Ras proteins bind to a protein kinase C-Raf-1 and activate the Raf-1 proteins. The activated
Raf-1 kinase subsequently phosphorylates MAP kinase kinases which, in turn, activate MAP
5 kinase ERKs by phosphorylating the threonine and tyrosine residues of the ERKs.
ERKs are proline-directed protein kinases which phosphorylate Ser/Thr-Pro motifs.
In fact, cytoplasmic phospholipase A2 (cPLA2) and transcription factor Elk-1 are substrates of
the ERKs. The ERKs phosphorylate Ser505 of cPLA2 and cause an increase in its enzymatic
activity resulting in an increased release of arachidonic acid and the formation of
1 0 Iysophospholipids from membrane phospholipids. Likewise, phosphorylation of the
transcription factor Elk-1 by ELK ultimately results in increased transcriptional activity.
MAP Kinase Subgroup JNK
An analysis of a deduced primary sequence of the two isoforms of JNK, 46 kDa and 55
kDa, reveals that they are distantly related to the ELK subgroup. They are similarly activated
by dual phosphorylation of Thr and Tyr, and the MKK4, MAP kinase kinases (Davis R (1994)
TIBS 19:470-473). The JNK signal transduction pathway can also be initiated by ultraviolet
light, osmotic stress, and the pro-inflammatory cytokines, TNF and IL-1. The Ras proteins
may partially activate the JNK signal transduction pathway. JNKs phosphorylate Ser63 and
Ser73 in the amino-terminal domain of the transcription factor c-Jun which results in
increased transcriptional activity.
MAP Kinase Subgroup p38
An analysis of the cDNA sequence encoding p38 shows that p38 is a 41 kD protein
containing 360 amino acids. Its dual phosphorylation is activated by the MAP kinase kinases,
MKK3 and MKK4. The p38 signal transduction pathway is also activated by heat shock,
hyperosmolar medium, IL-1 or LPS endotoxin (Han J et al (1994) Science 265:808-811)
produced by invading gram-negative bacteria. The human body reacts to the invading bacteria
by activating cells in the immune and inflammatory systems to initiating the systemic response
called sepsis. Sepsis is characterized by fever, chills, tachypnea, and tachycardia, and severe
cases may result in septic shock which includes hypotension and multiple organ failure.
LPS may be thought of as a stress signal to the cell because it alters normal cellular
processes by inducing the release of mediators such as TNF which has systemic effects. CD14 is
a glycosylphosphatidyl-inositol-anchored membrane glycoprotein which serves as an LPS
receptor on the plasma membrane of cells of monocytic origin. The binding of LPS to CD14
causes rapid protein tyrosine phosphorylation of the 44- and 42- or 40-kD isoforms of MAP
3 5 kinases. Although they bind LPS, these MAP kinase isoforms do not appear to belong to the p38
W0 97/02347 ~ 7 ~ ~ PCTIUS96/11170
subgroup.
Other MAP Kinase Homologs
Recent research (Lee JC et al (1994) Nature 372:739-745) has revealed that a newseries of pyridinyl-imidazole compounds, which inhibit LPS-mediated human monocyte IL-1
and TNF-o~ production actually work through a pair of closely related MAP kinase homologs,
termed cytokine suppressive binding proteins (CSBPs). These compounds are cytokine-
suppressive anti-inflammatory drugs (CSAlDs) which prevent phosphorylation and subsequent
cytokine biosynthesis. A comparison of fragments of CSBP sequences with those of MAP kinases
shows that genes encoding CSBPs are novel although related to protein serine/threonine kinases.
1 o It appears that CSBP proteins may be critical for cytokine production during human immune or
inflammatory reactions.
Understanding the mechanism for blocking the specific kinase activities may provide a
new way of treating inflammatory illnesses. Likewise, a thorough understanding of the various
MAP kinase signaling pathways can enable scientists to better understand cell signaling in other
1 5 developmental and disease processes. Identification of novel MAP kinases provides the
opportunity to diagnose or intervene in such disease processes.
DISCLOSURE OF THE INVENTION
The subject invention provides a unique nucleotide sequence, herein designated in lower
case, smap (SEQ ID NO:1) which encodes a novel human MAP kinase protein, designated in upper
case, SMAP (SEQ ID NO:2). The cDNA encoding SMAP was identified and cloned using Incyte
Clone No. 214915 from a stomach cDNA library.
The invention also relates to the use of the nucleotide and amino acid sequences of SMAP,
or its variants, in the diagnosis and treatment of activated or inflamed cells and/or tissues
associated with its expression. Aspects of the invention include the antisense DNA of smap;
cloning or expression vectors containing smap; host cells transformed with the expression
vector; a method for the production and recovery of purified SMAP from host cells; and purified
protein, SMAP, which can be used to produce antibodies or identify inhibitors of the protein.
BRIEF DESCRIPTION OF DRAWINGS
Figure 1A and 1B display the alignment of the nucieotide sequence (SEQ ID NO:1) and
amino acid sequence (SEQ ID NO:2) for human MAP kinase homolog produced using MacDNAsis
software (Hitachi Software Engineering Co Ltd).
Figure 2 shows the amino acid alignment between SMAP and mouse kinase, GenBank
531125 (locus MMU10871; Han et al. (1994) Science 265:808-810).
W097/02347 2 ~ 9 8 7 2 9 PCT/US96/11170
Figure 3 shows the amino acid alignment between SMAP and the closely related mitogen
activated protein kinase homolog, GenBank 603917 (locus HUMCSBP1; Lee et al (1994)
Nature 372:739-746). Alignments for Figs. 2 and 3 were produced using the INHERITT~ 670
Sequence Analysis System (Applied Biosystems, Foster City CA).
MODES FOR CARRYING OUT THE INVENTION
Defi nitions
As used herein, the lowercase letters, "smap", refer to a gene, cDNA or nucleic acid
1 o sequence for the novel human MAP kinase homolog while the uppercase letters, "SMAP", refer
to the protein sequence encoded by human MAP kinase homolog.
The present invention provides a unique nucleotide sequence identifying a novel MAP
kinase homolog from human stomach cell, SEQ ID NO:1. The coding region of SEQ ID NO:1 begins
at nucleotide 58 and ends at nucleotide 1156. Since SMAP is specifically involved with
1 5 protective cell signaling processes, the nucleic acid, protein, and antibodies are useful in the
study, diagnosis and treatment of conditions which affect the stomach such as gastritis, ulcers,
viral and bacterial infections, neoplasms and the like.
An "oligonucleotide" is a stretch of nucleotide residues which has a sufficient number of
bases to be used as an oligomer, amplimer or probe in a polymerase chain reaction (PCR).
Oligonucleotides are prepared from genomic or cDNA sequence and are used to amplify, confirm,
or reveal the presence of smap DNA or RNA in a particular cell or tissue. Oligonucleotides or
oligomers comprise portions of a DNA sequence having at least about 10 nucleotides and as many
as about 50 nucleotides, preferably about 15 to 30 nucleotides.
"Probes" are nucleic acid sequences of variable length, preferably between 10 and
6,000 nucleotides, which may be chemically synthesized, naturally occurring, or recombinant
single- or double-stranded nucleic acids. They are useful in the qualitative or quantitative
detection of the same, a similar, or a complementary nucleic acid sequence.
"Reporter" molecules are chemical moieties used for labelling a nucleic or amino acid
sequence. They include, but are not limited to, radionuclides, enzymes, fluorescent, chemi-
luminescent, or chromogenic agents. Reporter molecules associate with, est~hlish the presence
of, and may allow quantification of a particular nucleic or amino acid sequence.A "portion" or "fragment" of a polynucleotide or nucleic acid comprises all or any part
of the nucleotide sequence having fewer nucleotides than about 6 kb, preferably fewer than
about 1 kb which can be used as a probe. Such probes may be labeled with reporter molecules
using nick translation, Klenow fill-in reaction, PCR or other methods well known in the art.
WO 97/02347 2 ~ ~ ~ 7 2 9 PCT~Sg6/11170
After pretesting to optimize reaction conditions and to e' ,li"ate false positives, nucleic acid
probes may be used in Southern, northern or in situ hybridi~alions to determine whether DNA
or RNA encoding the protein is present in a biological sample, cell type, tissue, organ or
organism.
"Recombinant nucleotide variants" are polynucleotides which encode SMAP. They may
be synthesized by making use of the "redundancy" in the genetic code. Various codon
substitutions, such as the silent changes which produce specific restriction sites or codon
usage-specific mutations, may be introduced to optimize cloning into a plasmid or viral vector
or expression in a particular prokaryotic or eukaryotic host system, respectively.
"Linkers" are synthesized palindromic oligomers which create internal restriction
endonuclease sites.
"Chimeric" genes are polynucleotides which may be constructed by introducing all or
part of the nucleotide sequence of this invention into a vector containing additional nucleic acid
sequence(s). Such sequences may be expected to change any one (or more than one) of the
following SMAP characteristics: cellular location, distribution, ligand-binding affinities,
interchain affinities, degradation/turnover rate, signalling, etc.
"Active" refers to those forms, fragments, or domains of any SMAP polypeptide which
display the biologic and/or immunogenic activities of any naturally occurring SMAP.
"Naturally occurring SMAP" refers to a polypeptide produced by cells which have not
been genetically engineered and specifically contemplates various polypeptides which arise
from post-translational modifications. Such modi~icalions of the polypeptide include but not
limited to acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation.
"Derivative" refers to those polypeptides which have been chemically modified by such
techniques as ubiquitination, labelling (see above), pegylation (derivatization with
polyethylene glycol), and chemical insertion or substitution of amino acids such as ornithine
which do not normally occur in human proteins.
"Recombinant polypeptide variant" refers to any polypeptide which differs from
naturally occurring SMAP by amino acid insertions, deletions and/or substitutions, created
using recor"~ nanl DNA techniques. Guidance in determining which amino acid residues may be
replaced, added or deleted without abolishing activities of interest may be found by comparing
the sequence of SMAP with that of related polypeptides and ",i" "i~i"g the number of amino acid
sequence changes made in highly conserved regions.
Amino acid "substitutions" are defined as one for one amino acid replacements. They are
conservative in nature when the substituted amino acid has similar structural and/or chemical
properties. Examples of conservative replacements are suhstitution of a leucine with an
WO 97/02347 2 7 ~ 8 7 2 ~ PCT/US96/11170
isoleucine or valine, an aspartate with a glutamate, or a threonine with a serine.
Amino acid "insertions" or "deletions" are changes to or within an amino acid sequence.
They typically fall in the range of about 1 to 5 amino acids. The variation allowed in a
particular amino acid sequence may be experimentally determined by producing the peptide
synthetically or by systematically making insertions, deletions, or substitutions of nucleotides
in the smap sequence using reco",~ nant DNA te~;l,n.~_es.
A "signal or leader sequence" is a short amino acid sequence which or can be used, when
desired, to direct the polypeptide through a membrane of a cell. Such a sequence may be
naturally present on the polypeptides of the present invention or provided from heterologous
0 sources by recombinant DNA techn.~ues.
An "oligopeptide" is a short stretch of amino acid residues and may be expressed from an
oligonucleotide. It may be functionally equivalent to and the same length as (or considerably
shorter than) a "fragment," "portion," or "segment" of a polypeptide. Such sequences comprise
a stretch of amino acid residues of at least about 5 amino acids and often about 17 or more amino
1 5 acids, typically at least about 9 to 13 amino acids, and of sufficient length to display biologic
and/or immunogenic activity.
An "inhibitor" is a substance which retards or prevents a chemical or physiological
reaction or response. Common inhibitors include but are not limited to antisense molecules,
antibodies, and antagonisl~.
A "standard" is a quantitative or qualitative measurement for comparison. It is based on
a st~ti.stic~lly appropriate number of normal samples and is created to use as a basis of
comparison when performing diagnostic assays, running clinical trials, or following patient
treatment profiles.
"Animal" as used herein may be defined to include human, domestic (cats dogs, etc.),
agricultural (cows, horses, sheep, etc) or test species (mouse, rat, rabbit, etc).
Kinase nucleotide sequences have numerous appl - ons in techniques known to those
skilled in the art of molecular biology. These techniques include the use of kinase sequences as
hybridization probes, for chromosome and gene mapping, in the design of oligomers for PCR,
and in the production of sense or antisense nucleic acids, their chemical analogs and the like.
These examples are well known and are not intended to be limiting. Furthermore, the nucleotide
sequences disclosed herein may be used in molec~ r biology techniques that have not yet been
developed, provided the new techniques rely on properties of nucleotide sequences that are
currently known such as the triplet genetic code, specific base pair interactions, etc.
As a result of the degeneracy of the genetic code, a multitude of kinase-encoding
3 5 nucleotide sequences may be produced and some of these will bear only minimal homology to the
W097t02347 2 ~ 9 8 7 2 9 PCTtUS96tlll70
endogenous sequence of any known and naturally occurring kinase. This invention has
specifically contelllplated each and every possible variation of nucleotide sequence that could be
made by selecting combinations based on possible codon choices. These co",b..,alions are made in
accordance with the standard triplet genetic code as applied to the nucleotide sequence of
naturally occurring kinases, and all such variations are to be considered as being specifically
disclosed.
Although the nucleotide sequences which encode a specific kinase and its derivatives or
variants are preferably capable of identifying the nucleotide sequence of the naturally
occurring kinase under optimized conditions, it may be advantageous to produce smap possessing
a substantially different codon usage. Codons can be selected to increase the rate of peptide
expression in a particular prokaryotic or eukaryotic expression host in accordance with the
frequency with which particular codons are utilized by the host. Other reasons for
sub:,lantially altering the nucleotide sequence encoding the kinase without altering the encoded
amino acid sequence include the production of RNA ll~nsc,i~, having more desirable
properties, such as a longer half-life, than transcripts produced from the naturally occurring
sequence.
Nucleotide sequences encoding a kinase may be joined to a variety of other nucleotide
sequences by means of well est~' shed recombinant DNA techniques (Sambrook J et al (1989)
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor
NY; or Ausubel FM et al (1989) Current Protocols in Molecular Biology, John Wiley & Sons,
New York City). Useful nucleotide sequences for joining to the kinase include an assortment of
cloning vectors such as plas",;ds, cosmids, lambda phage derivatives, phagemids, and the like.
Vectors of interest include vectors for replication, expression, probe generation, sequencing,
and the like. In general, vectors of interest may contain an origin of replication functional in at
least one organism, convenient restriction endonuclease sensitive sites, and selectable markers
for one or more host cell systems.
Another aspect of the subject invention provides for kinase hybridization probes which
are capable of hybridizing with naturally occurring nucleotide sequences encoding kinases. The
stringency of the hybridization conditions will determine whether the probe identifies only
nucleotide sequence of that specific kinase or sequences of closely related molecules. If such
probes are used for the detection of related kinase encoding sequences, they should preferably
contain at least ~0% of the nucleotides from any of the sequence presented here. Hybridization
probes of the subject invention may be derived from the nucleotide sequences of the SEQ ID NO:1
or from an isolated genomic sequence including untranslated regions such as promoters,
enhancers and introns. Such hyL,idi~alion probes may be labeled with reporter molecules.
~ 2 ~ ~ 8 7 ~ 9
WO 97/02347 PCT/US96/11170
PCR as described US Patent Nos. 4,683,195; 4,800,195; and 4,965,188 provides
additional uses for oligonucleotides based upon the kinase nucleotide sequence. Such oligomers
may be of recombinant origin, chemically synthesized, or a mixture of both. Oligomers may
comprise two nucleotide sequences el",~!oyed under opli",i~ed conditions for tissue specific
identification or diagnostic use. The same two oligomers, nested sets of oligomers, or even a
degenerate pool of oligomers may be employed under less stringent conditions for identification
of closely related DNA or RNA sequences.
Full length genes may be cloned from known sequence using a new method disclosed in
Patent Application serial No. 08/487,112 filed June 7, 1995 and hereby incorporated by
1 o reference, which employs XL-PCR (Perkin-Elmer, Foster City, CA) to amplify long pieces of
DNA. This method was developed to allow a single researcher to process multiple genes (up to
20 or more) at a time and to obtain an extended (possibly full-length) sequence within 6-10
days. It replaces current methods which use labeled probes to screen libraries and allow one
researcher to process only about 3-5 genes in 14-40 days.
1 5 In the first step, which can be performed in about two days, primers are designed and
synthesized based on a known partial sequence. In step 2, which takes about six to eight hours,
the sequence is extended by PCR a",pli~icalion of a selected library. Steps 3 and 4, which take
about one day, are purification of the amplified cDNA and its ligation into an appropriate vector,
respectively. Step 5, which takes about one day, involves l~ans~orr"i.~g and growing up host
bacteria. In step 6, which takes approximately five hours, PCR is used to screen bacterial
clones for extended sequence. The final steps, which take about one day, involve the preparation
and sequencing of selected clones. If the full length cDNA has not been obtained, the entire
procedure is repeated using either the original library or some other preferred library. The
preferred library may be one that has been size-selected to include only larger cDNAs or may
consist of single or combined commercially available libraries, eg. Iung, liver, heart and brain
from Gibco/BRL (Gaithersburg MD). The cDNA library may have been prepared with oligo
d(T) or random primers. The advantage of using random primed libraries is that they will have
more sequences which contain 5' ends of genes. A randomly primed library may be particularly
useful if an oligo d(T) library does not yield a complete gene. Obviously, the larger the protein,
the less likely it is that the complete gene will be found in a single plasmid.
Other means of producing specific hybridization probes for kinases include the cloning
of the cDNA sequences into vectors for the production of mRNA probes. Such vectors are known
in the art, are commercially available, and may be used to synthesize RNA probes in vitro by
addition of an appropriate RNA polymerase such as T7 or SP6 and labeled nucleotides.
It is possible to produce a DNA sequence, or portions thereof, entirely by synthetic
WO 97/02347 ~ 2 ~ PCT/US96111170
chemistry. After synthesis, the nucleic acid sequence can be inserted into any of the many
available DNA vectors and their respective host cells using techniques which are well known in
the art. Moreover, synthetic chemistry may be used to introduce mutations into the nucleotide
sequence. Alternately, a portion of sequence in which a mutation is desired can be synthesized
and recombined with a portion of an existing genomic or r~co",':.,ant sequence.
The kinase nucleotide sequences can be used individually, or in panels, in an assay to
detect inflammation or disease associated with abnormal levels of kinase expression. The
nucleotide sequence is added to a fluid, cell or tissue sample from a patient under hybridi~i"g
conditions. After an incubation period, the sample is washed with a compatible fluid which
optionally contains a reporter molecule which will bind the specific nucleotide. After the
compatible fluid is rinsed off, the reporter molecule is quantitated and compared with a
standard for that fluid, cell or tissue. If kinase ek~ression is significantly different from the
standard, the assay indicates the presence of inflammation or disease.
This same assay, colllbil~ 19 a sample with the nucleotide sequence, is applicable in
evaluating the efficacy of a particular therapeutic treatment regime. It may be used in animal
studies, in clinical trials, or in monitoring the treatment of an individual patient. First,
standard expression must be established for use as a basis of co""~ari~on. Second, samples from
the animals or patients affected by the disease are combined with the nucleotide sequence to
evaluate the deviation from the standard or normal profile. Third, an existing therapeutic agent
is administered, and a l,t:all"ent profile is generated. The assay is evaluated to determine
whether the profile progresses toward or returns to the standard pattern. Successive treatment
profiles may be used to show the effects of treatment over a period of several days or over
several months.
The cDNA for human MAP kinase can also be used to design hybridization probes for
2 5 mapping the native genomic sequence. The sequence may be mapped to a particular chromosome
or to a specific region of the chromosome using well known techniques. These include in situ
hybridization to chromosomal spreads (Verma et al (1988) Human Chromosomes: A Manual of
Basic Techniques, Pergamon Press, New York City), flow-sorted chromosomal preparations, or
artificial chromosome constructions such as yeast artificial chromosomes (YACs), bacterial
artificial chromosomes (BACs), bacterial P1 constructions or single chromosome cDNA
libraries.
In situ hybridization of chromosomal preparations and physical mapping techniques
such as linkage analysis using established chromosomal markers are invaluable in extending
genetic maps. Examples of genetic map data can be found in the 1994 Genome Issue of Science
(265:1981f). Often the placement of a gene on the chromosome of another mammalian species
0 2 ~ 9 8 7 2 9
WO 97/02347 PCT/US96/11170
may reveal associated markers even if the number or arm of a particular human chromosome is
not known. New nucleotide sequences can be assigned to chromosomal subregions by physical
mapping. This provides valuable i"~or-~ation to investigators searching for disease genes using
positional cloning or other gene discovery techniques. Once a disease or syndrome, such as
ataxia telan~iect~cia (AT), has been crudely localized by genetic linkage to a particular genomic
region, for example, AT to 11q22-23 (Gatti et al (1988) Nature 336:577-580), anysequences mapping to that area may represent genes for further investig~tion of AT. The
nucleotide sequence of the subject invention may also be used to detect differences in gene
sequence between normal and carrier or affected individuals.
1 0 Nucleotide sequences encoding a particular kinase may be used to produce purified
oligopeptide using well known methods of recombinant DNA technology. Goeddel (1990, Gene
Expression Technology, Methods and Enzymology, Vol 185, Academic Press, San Diego CA) is
one among many publications which teach expression of an isolated nucleotide sequence. The
oligopeptide may be expressed in a variety of host cells, either prokaryotic or eukaryotic. Host
1 5 cells may be from the same species from which the nucleotide sequence was derived or from a
different species. Advantages of producing an oligonucleotide by recombinant DNA technology
include obtaining adequate amounts of the protein for purification and the availability of
simplified purification procedures.
Cells transformed with a kinase nucleotide sequence may be cultured under conditions
suitable for the expression and recovery of the oligopeptide from cell culture. The oligopeptide
produced by a recombinant cell may be secreted or may be contained intracellularly depending
on the sequence and the genetic construction used. In general, it is more convenient to prepare
recombinant proteins in secreted form. Purification steps vary with the production process
and the particular protein produced. Often an oligopeptide can be produced from a chimeric
nucleotide sequence. This is accomplished by ligating the kinase sequence to a nucleic acid
sequence encoding a polypeptide domain which will facilitate protein purification (Kroll DJ et
al (1993) DNA Cell Biol 12:441-53).
In addition to recombinant or chimeric production, kinase fragments may be produced by
direct peptide synthesis using solid-phase techniques (Stewart et al (1969) Solid-Phase
Peptide Synthesis, WH Freeman Co, San Francisco CA; Merrifield J (1963) J Am Chem Soc
85:2149-2154). Automated synthesis may be achieved, for example, using Applied
Biosystems 431A Peptide Synthesizer in accordance with the instructions provided by the
manufacturer. Additionally a particular kinase sequence, or any part thereof, may be mutated
during chemical synthesis, combined using chemical methods with other kinase sequence(s),
and used in an appropriate vector and host cell to produce a polypeptide.
1 0
~27 ~87~
WO 97/02347 PCTJUS96/11170
Although the amino acid sequence or oligopeptide used for antibody induction does not
require biological activity, it must be antigenic and consist of at least five amino acids and
preferably at least 10 amino acids. Short stretches of amino acid sequence may be fused with
those of another protein such as keyhole limpet hemocyanin, and the chimeric peptide used for
antibody production.
Antibodies specific for SMAP may be produced by inoculation of an appropriate animal
with an antigenic fragment of the peptide. An antibody is specific for SMAP if it is produced
against an epitope of the polypeptide and binds to at least part of the natural or recombinant
protein. Antibody production includes not only the stimulation of an immune response by
1 o injection into animals, but also analogous processes such as the production of synthetic
antibodies, the screening of recombinant immunoglobulin libraries for specific-binding
molecules (Orlandi R et al (1989) PNAS 86:3833-3837, or Huse WD et al (1989) Science
256:1275-1281), or the in vitro stimulation of Iymphocyte populations. Current technology
(Winter G and Milstein C (1991) Nature 349:293-299) provides for a number of highly
1 5 specific binding reagents based on the prin- p!es of antibody fo""alion. These techniques may
be adapted to produce molecules which specifically bind SMAPs.
The examples below are provided to illustrate the subject invention. These examples are
provided by way of illustration and are not included for the purpose of limiting the invention.
2 0 INDUSTRIAL APPLICABILITY
Isolation of mRNA and Construction of the cDNA Library
The partial cDNA sequence for the human MAP kinase homolog was initially identified in
Incyte Clone 214915 among the sequences comprising the human stomach cell library, Patent
Application Serial Number 08/385,268, filed 7 February 1995, disclosed herein byreference. The normal stomach tissue used for this library was obtained from the Keystone
Skin Bank, International Institute for the Advancement of Medicine (Exton PA).
Five grams of normal stomach tissue from a 55 year old male (KSP93-B72) was flash
frozen, ground in a mortar and pestle, and Iysed immediately in buffer containing guanidinium
isothiocyanate. Lysis was followed by centrifugation through cesium chloride, incubation with
DNase and ethanol precipitation.
The RNA was sent to Stratagene (La Jolla CA) and oligo d(T) priming was used to prepare
the cDNA library. Synthetic linkers were ligated onto the cDNA molecules, and they were
inserted into the Uni-ZAPTM vector system (Stratagene).
02~ 98729
WO 97/02347 rcTlus96llll7o
I I Isolation of cDNA Clones
The phagemid forms of individual cDNA clones were obtained by the in vivo excision
process, in which the host bacterial strain was co-infected with both the library phage and an
f1 helper phage. Polypeptides or enzymes derived from both the library-containing phage and
the helper phage nicked the DNA, initiated new DNA synthesis from defined sequences on the
target DNA, and created a smaller, single stranded circular phagemid DNA molecule that
included all DNA sequences of the pBluescript phagemid and the cDNA insert. The phagemid DNA
was released from the cells, purified, and used to reinfect fresh host cells (SOLR, Stratagene)
where double-stranded phagemid DNA was produced.
1 o Phagemid DNA was purified using the QIAWELL-8~M Plasmid Purification System
(QIAGEN Inc, Chatsworth CA). This product Iyses bacterial cells and allows the isolation of
highly purified phagemid DNA using QIAGEN anion-exchange resin particles in a multiwell
format. The DNA was eluted from the purification resin and prepared for DNA sequencing and
other analytical manipulations.
1 5 An alternate method of purifying phagemid utilizes the Miniprep Kit (Catalog No.
77468; Advanced Genetic Technologies Corp, Gaithersburg MD). The kit has a 96-well format
and provides enough reagents for 960 pu,i~icdlions. The reco"""ended protocol is employed
except for the following changes. First, each of the 96 wells is filled with 1 ml of sterile
terrific broth (LIFE TECHNOLOGIESTM, Gaithersburg MD) containing carbenicillin at 25 mg/L
and glycerol at 0.4%. The bacteria are introduced into the wells, cultured for 24 hours and
Iysed with 60 1ll of Iysis buffer. The block is centrifuged at 2900 rpm for 5 minutes and then
the contents of the block are added to the primary filter plate. An optional step of adding
isopropanol to the TRIS buffer is not routinely performed. Following the last step in the
protocol, samples are transferred to a Beckman 96-well block for storage.
lll Sequencing of cDNA Clones
The cDNA inserts from random isolates of the stomach library were sequenced in part.
Methods for DNA sequencing are well known in the art and employ such enzymes as SEQUENASE(g
(US Biochemical Corp, Cleveland, OH) or Taq polymerase. Methods to extend the DNA from an
oligonucleotide primer annealed to the DNA ~eri,pldle of interest have been developed for the use
of both single- and double-stranded templates. The chain termination reaction products were
separated using electrophoresis and urea-acrylamide gels and detected either by
autoradiography with radionuclide-labeled precursors or by fluorescent or chromogenic
labelling. Recent improvements in mechanized reaction preparation, sequencing and analysis
using the latter methods have permitted expansion in the number of sequences determined per
WO 97/02347 ~ 8 7 2 ~ PCT/US96/11170
day. The machines used in these processes include the Catalyst 800,11ar"illon Micro Lab 2200
(Hamilton, Reno NV), Peltier Thermal Cycler (PTC200; MJ Research, Watertown MA) and the
Applied Biosystems 377 and 373 DNA sequencers.
IV Homology Searching of cDNA Clones and Deduced Proteins
Each sequence so obtained was co" ,pared to sequences in GenBank using a search
algorithm developed by Applied Biosystems and i"cor~,oraled into the INHERIT 670 Sequence
Analysis System. In this algorithm, Pattern Specification Language (developed by TRW Inc, Los
Angeles CA) was used to determine regions of homology. The three parameters that determine
1 o how the sequence comparisons run were window size, window offset, and error tolerance. Using
a co",t..,a~ion of these three parameters, the DNA database was searched for sequences
containing regions of homology to the query sequence, and the appropriate sequences were
scored with an initial value. Subsequently, these homologous regions were examined using dot
matrix homology plots to distinguish regions of homology from chance matches.
1 5 Smith-Waterman alignments were used to display the results of the homology search.
Peptide and protein sequence homologies were ascertained using the INHERITTM 670Sequence Analysis System in a way similar to that used in DNA sequence homologies. Pattern
Specification Language and parameter v.;.ldo,/~s were used to search protein d~t~h~.ces for
sequences containing regions of homology which were scored with an initial value. Dot-matrix
homology plots were examined to distinguish regions of siyl~ callt holllcloyy from chance
~alches.
Alternatively, BLAST, which stands for Basic Local Alignment Search Tool, is used to
search for local sequence alignments (Altschul SF (1993) J Mol Evol 36:290-300; Altschul,
SF et al (1990) J Mol Biol 215:403-10). BLAST produces alignments of both nucleotide and
amino acid sequences to determine sequence similarity. Because of the local nature of the
alignments, BLAST is especially useful in determining exact matches or in identifying homologs.
Whereas it is ideal for matches which do not contain gaps, it is inappropriate for performing
motif-style searching. The fundamental unit of BLAST algorithm output is the High-scoring
Segment Pair (HSP).
An HSP consists of two sequence fragments of arbitrary but equal lengths whose
alignment is locally maximal and for which the alignment score meets or exceeds a threshold or
cutoff score set by the user. The BLAST approach is to look for HSPs between a query sequence
and a d~t~h~ce sequence, to evaluate the statistical siyl ,i~icance of any matches found, and to
report only those matches which satisfy the user-selected threshold of significance. The
parameter E establishes the statistically significant threshold for reporting database sequence
~ 2 ~ 2 9
WO 97/02347 PCT/US96/11170
matches. E is i,lter~reted as the upper bound of the expected frequency of chance occurrence of
an HSP (or set of HSPs) within the context of the entire database search. Any cl~t~h~ce sequence
whose match satisfies E is reported in the program output.
V Extension of the cDNA to Full Length
Analysis of the INHERITTM results from the randomly picked and sequenced portions of
clones from the stomach library identified Incyte 214915 as a homolog of MAP kinase. The
cDNA of Incyte 214915 was extended to full length using a modified XL-PCR (Perkin Elmer)
procedure. Primers were designed based on the known sequence; one primer was synthesized to
1 o initiate extension in the antisense direction (XLR) and the other to extend sequence in the sense
direction (XLF). The primers allowed the sequence to be extended "outward" generating
amplicons containing new, ullh.lo~"l nucleotide sequence for the gene of interest. The primers
were designed using Oligo 4.0 (National Biosciences Inc, Plymouth MN) to be 22-30
nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence
1 5 at temperatures about 68-72 C. Any stretch of nucleotides which would result in hairpin
structures and primer-primer dimerizations was avoided.
The ~o" ,ach cDNA library was used as a te" Ipldlt3, and XLR = MG ACA TCC AGG AGC CCA
ATG AC and XLF = AGG TGA TCC TCA GCT GGA TGC AC primers were used to extend and amplify the
214915 sequence. By following the instructions for the XL-PCR kit and thoroughly mixing the
enzyme and reaction mix, high fidelity amplification is obtained. Beginning with 25 pMol of
each primer and the recommended concenl,~lions of all other components of the kit, PCR was
performed using the Peltier thermal cycler (MJ PTC200; MJ Research, Watertown MA) and
the following parameters:
Step 1 94 C for 60 sec (initial denaturation)
Step 2 94 C for 15 sec
Step 3 65 C for 1 min
Step 4 68 C for 7 min
Step 5 Repeat step 2-4 for 15 additional times
Step 6 94 C for 15 sec
Step 7 65 C for 1 min
Step 8 68 C for 7 min + 15 sec/cycle
Step 9 Repeat step 6-8 for 11 additional times
Step 10 72 C for 8 min
Step 11 4 C (and holding)
7 ~ ~
WO 97/02347 PCTIUS96/11170
At the end of 28 cycles, 50 ~l of the reaction mix was removed; and the remaining
reaction mix was run for an additional 10 cycles as outlined below:
Step 1 94 C for 15 sec
Step 2 65 C for 1 min
Step 3 68 C for (10 min + 15 sec)/cycle
Step 4 Repeat step 1-3 for 9 additional times
Step 5 72 C for 10 min
A 5-10 ~l aliquot of the reaction mixture was analyzed by electrophoresis on a low
concentration (about 0.6-0.8%) agarose mini-gel to determine which reactions were
10 successful in extending the sequence. Although all extensions potentially contain a full length
gene, some of the largest products or bands were selected and cut out of the gel. Further
purification involved using a commercial gel extraction method such as QlAQuickTM (QIAGEN
Inc). After recovery of the DNA, Klenow enzyme was used to trim single-stranded, nucleotide
overhangs creating blunt ends which facilitated religation and cloning.
After ethanol precipitation, the products were redissolved in 13 ~11 of ligation buffer.
Then, 1111 T4-DNA ligase (15 units) and 1~11 T4 polynucleotide kinase were added, and the
mixture was incubated at room temperature for 2-3 hours or overnight at 16 C. Competent E.
coli cells (in 40 ~LI of appropriate media) were transformed with 3 1ll of ligation mixture and
cultured in 80 1ll of SOC medium (Sambrook J et al, supra). After incubation for one hour at
37 C, the whole transformation mixture was plated on Luria Bertani (LB)-agar (Sambrook J
et al, supra) containing carbenicillin at 25 mg/L. The following day, 12 colonies were
randomly picked from each plate and cultured in 150 ~l of liquid LB/carbenicillin medium
placed in an individual well of an appropriate, commercially-available, sterile 96-well
microtiter plate. The following day, 5 1ll of each overnight culture was transferred into a non-
sterile 96-well plate and after dilution 1:10 with water, 5 ~l of each sample was transferred
into a PCR array.
For PCR amplification, 15 ~l of concentrated PCR reaction mix (1.33X) containing0.75 units of Taq polymerase, a vector primer and one or both of the gene specific primers used
for the extension reaction were added to each well. Amplification was performed using the
following conditions:
Step 1 94 C for 60 sec
Step 2 94 C for 20 sec
Step 3 55 C for 30 sec
Step 4 72 C for 90 sec
Step 5 Repeat steps 2-4 for an additional 29 times
1 5
~2~ ~7~9
WO 97/02347 PCT/US96/11170
Step 6 72 C for 180 sec
Step 7 4 C (and holding)
Aliquots of the PCR reactions were run on agarose gels together with molecular weight
markers. The sizes of the PCR products were compared to the original partial cDNAs, and
5 appropriate clones were selected, ligated into plasmid and sequenced.
When the three possible amino acid translalions of the full length cDNA sequence were
searched against protein ~t~hases such as SwissProt and PIR, no exact matches were found.
Figure 1 shows the nucleotide and amino acid sequences for human MAP kinase homolog. The
alignment of the amino acid sequence for SMAP (SEQ ID NO: 2) with MMU10871 (Gl 531125,
1 o SEQ ID NO:3) and HUMCSBP1(GI 603917) are shown in Figs 2 and 3, respectively.
Vl Sense or Antisense Molecules
Knowledge of the correct cDNA sequence of any particular kinase, or part thereof,
enables its use as a tool in sense or antisense technologies for the invealigation of gene function.
1 5 Oligonucleotides, from genomic or cDNAs, comprising either the sense or the antisense strand of
the cDNA sequence is used in vitro or in vivo to inhibit expression. Such technology is now well
known in the art, and oligonucleotides or other fragments are designed from various locations
along the sequences. The gene of interest is turned off in the short term by transfecting a cell or
tissue with ex~.ression vectors which flood the cell with sense or antisense sequences until all
20 copies of the vector are disabled by endogenous nucle~ses. Stable l,anslection of appropriate
germ line cells or a zygote with a vector containing the fragment produces a l,dnsgenic
organism (US Patent No. 4,736,866, 12 April 1988), whose cells produce enough copies of
the sense or antisense sequence to significantly co",pro",ise or entirely eliminate normal
activity of the particular kinase gene. Frequently, the function of the gene is ascertained by
25 observing behaviors such as lethality, loss of a phy.iologic~l pathway, changes in morphology,
etc at the intracellular, cellular, tissue or organismal level.
In addition to using fragments constructed to interrupt llansc,i~tion of the open reading
frame, modifications of gene expression are obtained by designing antisense sequences to
promoters, enhancers, introns, or even to transacting regulatory genes. Similarly, inhibition
30 is achieved using Hogeboom base-pairing methodology, also known as "triple helix" base
pairing .
Vll Expression of SMAP
Expression of smap is acco",plished by subcloning the cDNAs into apprupric.le
35 expression vectors and transfecting the vectors into an appropriate expression hosts. In this
~2~ 2~
WO 97/02347 PCTJUS96/11170
particular case, the cioning vector previously used for the generation of the tissue library also
provide for direct expression of smap sequences in E. coli. Up~l,ea"l of the cloning site, this
vector contains a promoter for r3-9~l~rtosidasel followed by sequence containing the
amino-terminal Met and the subsequent 7 residues of 13-galactosidase. Immediately following
5 these eight residues is an engineered bacteriophage promoter useful for artificial priming and
transcription and a number of unique restriction sites, including Eco Rl, for cloning.
Induction of the isolated, transfected bacterial strain with IPTG using standard methods
produces a fusion protein corresponding to the first seven residues of 13-g~l~ritosid~se, about 5
to 15 residues which correspond to linker, and the peptide encoded within the cDNA. Since cDNA
clone inserts are generated by an essentially random process, there is one chance in three that
the included cDNA lies in the correct frame for proper translation. If the cDNA is not in the
proper reading frame, it is obtained by deletion or insertion of the appropriate number of bases
by well known methods including in vitro mutagenesis, digestion with exonuclease lll or mung
bean nucle~.ce, or oligonucleotide linker inclusion.
The smap cDNA is shuttled into other vectors known to be useful for expression of
protein in specific hosts. Oligonucleotide linkers containing cloning sites as well as a segment
of DNA sufficient to hybridize to stretches at both ends of the target cDNA (25 bases) is
synthesized chemically by standard methods. These primers are then used to amplify the
desired gene segments by PCR. The resulting new gene segments are digested with appropriate
restriction enzymes under standard conditions and isolated by gel electrophoresis. Alternately,
similar gene segments are produced by digestion of the cDNA with appropriate restriction
enzymes and filling in the missing gene segments with che", --lly synthesized oligonucleotides.
Segments of the coding sequence from more than one gene are ligated together and cloned in
appropriate vectors to opli",i~e expression of recombinant sequence.
Suitable ex~,ression hosts for such chimeric molecules include but are not limited to
mammalian cells such as Chinese Hamster Ovary (CHO) and human 293 cells, insect cells such
as Sf9 cells, yeast cells such as Saccharomyces cerevisiae, and bacteria such as E. coli. For
each of these cell systems, a useful expression vector includes an origin of replication to allow
propagation in bacteria and a select~hlc marker such as the l3-lactamase antibiotic resistance
gene to allow selection in bacteria. In addition, the vectors include a second selectable marker
such as the neomycin phosphotransferase gene to allow selection in transfected eukaryotic host
cells. Vectors for use in eukaryotic expression hosts usually require RNA processing elements
such as 3' polyadenylation sequences if such are not part of the cDNA of interest.
Additionally, the vector contains promoters or enhancers which increase gene
expression. Such promoters are host specific and include MMTV, SV40, and metallothionine
~2~ ~729
WO 97/02347 PCT/US96/11170
promoters for CHO cells; trp, lac, tac and T7 promoters for bacterial hosts; and alpha factor,
alcohol oxidase and PGH promoters for yeast. Transc,i~lion enhancers, such as the rous
sarcoma virus (RSV) enhancer, is used in mammalian host cells. Once homogeneous cultures of
recombinant cells are obtained through standard culture methods, large quantities of
recombinantly produced SMAP are recovered from the conditioned medium and analyzed using
chromatographic methods known in the art.
Vlll Isolation of Recombinant SMAP
SMAP is expressed as a chimeric protein with one or more additional polypeptide
domains added to facilitate protein purification. Such purification-facilitating domains include,
but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow
purification on immobilized metals, protein A domains that allow purification on immobilized
immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system
(Immunex Corp, Seattle WA). The inclusion of a cleavable linker sequence such as Factor XA or
enterokinase (Invitrogen) between the purification domain and the smap sequence is useful to
facilitate purification of SMAP.
IX Production of SMAP Specific Antibodies
Two approaches are utilized to raise antibodies to SMAP, and each approach is useful for
generating either polyclonal or monoclonal antibodies. In one approach, denatured protein from
the reverse phase HPLC separation is obtained in quantities up to 75 mg. This denatured
protein is used to immunize mice or rabbits using standard protocols; about 100 micrograms
are adequate for immunization of a mouse, while up to 1 mg might be used to immunize a rabbit.
For identifying mouse hybridomas, the denatured protein is radioiodinated and used to screen
potential murine B-cell hybridomas for those which produce antibody. This procedure requires
only small quantities of protein, such that 20 mg would be sufficient for labeling and screening
of several thousand clones.
In the second approach, the amino acid sequence of SMAP, as deduced from translation of
the cDNA, is analyzed to determine regions of high immunogenicity. Oligopeptides co"~p~isi"g
appropriate hydrophilic regions are synthesized and used in suitable immunization protocols to
raise antibodies. Analysis to select appropriate epitopes is described by Ausubel FM et al
(supra). The optimal amino acid sequences for immunization are usually at the C-terminus,
the N-terminus and those intervening, hydrophilic regions of the polypeptide which are likely
to be exposed to the external environment when the protein is in its natural conformation.
Typically, selected peptides, about 15 residues in length, are synthesized using an
1 8
~ 2 ~` ~ 8 ~ ~ ~
WO 97/02347 PCT/US96/11170
Applied Biosystems Peptide Synthesizer Model 431A using fmoc-chemistry and coupled to
keyhole limpet hemocyanin (KLH, Sigma) by reaction with M-maleimidobenzoyl-N-
hydroxysucc;,li,llide ester (MBS; Ausubel FM et al, supra). If necessary, a cysteine is
introduced at the N-terminus of the peptide to permit coupling to KLH. Rabbits are immunized
with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested
for antipeptide activity by binding the peptide to plastic, blocking with 1% bovine serum
albumin, reacting with antisera, washing and reacting with labeled (radioactive or
fluorescent), affinity purified, specific goat anti-rabbit IgG.
Hybridomas are prepared and screened using standard techniques. Hybridomas of
interest are detected by screening with labeled SMAP to identify those fusions producing the
monoclonal antibody with the desired specificity. In a typical protocol, wells of plates (FAST;
Becton-Dickinson, Palo Alto, CA) are coated during incubation with affinity purified, specific
rabbit anti-mouse (or suitable anti-species lg) antibodies at 10 mg/ml. The coated wells are
blocked with 1% BSA, washed and incubated with supernatants from hybridomas. After washing
the wells are incubated with labeled SMAP at 1 mg/ml. Supernatants with specific antibodies
bind more labeled SMAP than is dele~ in the background. Then clones producing specific
antibodies are expanded and subjected to two cycles of cloning at limiting dilution (1 cell/3
wells). Cloned hybridomas are injected into pristane-treated mice to produce ascites, and
monoclonal antibody is purified from mouse ascitic fluid by affinity chromatography on Protein
A. Monoclonal antibodies with affinities of at least 108/M, preferably 109 to 1010 or stronger,
are typically made by standard procedures as described in Harlow and Lane (1988) Antibodies:
A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; and in Goding
(1986) Monoclonal Antibodies: Principles and Practice, Academic Press, New York City, both
incorporated herein by reference.
X Diagnostic Test Using SMAP Specific Antibodies
Particular SMAP antibodies are useful for investigation of various forms of stomach
conditions characterized by differences in the amount or distribution of SMAP. Given the usual
role of MAP kinases, SMAP from the human stomach library appears to be upregulated in its
characteristic involvement in immune protection or defense.
Diagnostic tests for SMAP include methods utilizing the antibody and a label to detect
SMAP in human body fluids, membranes, cells, tissues or extracts of such. The polypeptides
and antibodies of the present invention are used with or without modification. Frequently, the
polypeptides and antibodies are labeled by joining them, either covalently or noncovalently,
with a substance which provides for a detectable signal. A wide variety of labels and conjugation
1 9
WO 97/02347 2 ~ ~ ~ 7 2 ~ PCTIUS96/11170
techniques are known and have been reported extensively in both the scie~ ic and patent
literature. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors,
fluorescent agents, chemiluminescent agents, magnetic particles and the like. Patents teaching
the use of such labels include US Patent Nos. 3,817,837; 3,850,752; 3,939,350;
3,996,345; 4,277,437; 4,275,149; and 4,366,241. Also, recombinant immunoglobulins
are produced as shown in US Patent No. 4,816,567, incor~uo,~ted herein by reference.
A variety of protocols for measuring soluble or membrane-bound SMAP, using either
polyclonal or monoclonal antibodies specific for the protein, are known in the art. Examples
include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) and
1 o fluorescent activated cell sorting (FACS). A two-site monoclonal-based immunoassay utilizing
monoclonal antibodies reactive to two non-interfering epitopes on SMAP is preferred, but a
competitive binding assay may be employed. These assays are described, among other places, in
Maddox, DE et al (1983, J Exp Med 158:1211).
1 5 Xl Purification of Native SMAP Using Specific Antibodies
Native or recombinant SMAP is purified by immunoaffinity chromalogl~phy using
antibodies specific for SMAP. In general, an immunoaffinity column is constructed by
covalently coupling the anti-SMAP antibody to an activated chro",atoy~aphic resin.
Polyclonal immunoglobulins are prepared from immune sera either by precipitationwith ammonium sulfate or by purification on immobilized Protein A (Pharmacia LKBBiotechnology, Piscataway NJ). Likewise, monoclonal antibodies are prepared from mouse
ascites fluid by ammonium sulfate precipitation or cl,lulllalography on immobilized Protein A.
Partially purified immunoglobulin is covalently attached to a chromatographic resin such as
CnBr-activated Sepharose (Pharmacia LKB Biotechnology). The antibody is coupled to the
resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's
instructions .
Such immunoaffinity columns are utilized in the purification of SMAP by preparing a
fraction from cells containing SMAP in a soluble form. This preparation is derived by
solubilization of whole cells or of a subcellular fraction obtained via differential centrifugation
(with or without addition of detergent) or by other methods well known in the art.
Alternatively, soluble SMAP containing a signal sequence is secreted in useful quantity into the
medium in which the cells are grown.
A soluble SMAP-containing preparation is passed over the immunoaffinity column, and
the column is washed under conditions that allow the preferential absorbance of SMAP (eg, high
ionic strength buffers in the presence of detergent). Then, the column is eluted under
~2~ 7~
WO 97/02347 PCT/US96/11170
conditions that disrupt antibody/SMAP binding (eg, a buffer of pH 2-3 or a high concentration
of a chaotrope such as urea or thiocyanate ion), and SMAP is collected.
X l l Drug Screening
This invention is particularly useful for screening therapeutic compounds by using
SMAP or binding fragments thereof in any of a variety of drug screening techniques. The
polypeptide or fragment employed in such a test is either free in solution, affixed to a solid
support, borne on a cell surface or located intracellularly. One method of drug screening
utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant
0 nucleic acids ex~ressi,lg the polypeptide or fragment. Drugs are screened against such
transformed cells in competitive binding assays. Such cells, either in viable or fixed form, are
used for standard binding assays. One measures, for example, the formation of complexes
between SMAP and the agent being tested. Alternatively, one can examine the diminution in
complex formation between SMAP and a receptor caused by the agent being tested.
Thus, the present invention provides methods of screening for drugs or any other agents
which affect signal transduction. These methods comprise contacting such an agent with SMAP
polypeptide or a fragment thereof and assaying (i) for the presence of a complex between the
agent and the SMAP polypeptide or fragment, or (ii) for the presence of a complex between the
SMAP polypeptide or fragment and the cell, by methods well known in the art. In such
competitive binding assays, the SMAP polypeptide or fragment is typically labeled. After
suitable incubation, free SMAP polypeptide or fragment is separated from that present in bound
form, and the amount of free or uncomplexed label is a measure of the ability of the particular
agent to bind to SMAP or to interfere with the SMAP and agent cor~rl~x.
Another technique for drug screening provides high throughput screening for compounds
having suitable binding affinity to the SMAP polypeptides and is described in detail in European
Patent Application 84/03564, published on September 13, 1984, incorporated herein by
reference. Briefly stated, large numbers of different small peptide test compounds are
synthesized on a solid substrate, such as plastic pins or some other surface. The peptide test
compounds are reacted with SMAP polypeptide and washed. Bound SMAP polypeptide is then
detected by methods well known in the art. Purified SMAP may also be coated directly onto
plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing
antibodies can be used to capture the peptide and i~""obili~e it on the solid support.
This invention also contemplates the use of competitive drug screening assays in which
neutralizing antibodies capable of binding SMAP specifically compete with a test compound for
binding to SMAP polypeptides or fragments thereof. In this manner, the antibodies are used to
W097/02347 2 ~ ~ 8 ~ 2 9 PCT/USg6/11170
detect the presence of any peptide which shares one or more antigenic determinants with SMAP.
Xlll Rational Drug Design
The goal of rational drug design is to produce structural analogs of biologically active
polypeptides of interest or of small molecules with which they interact, e.g., agonists,
antagonists, or inhibitors. Any of these examples are used to fashion drugs which are more
active or stable forms of the polypeptide or which enhance or interfere with the function of a
polypeptide in vivo (Hodgson J (1991) Bio/Technology 9:19-21, incorporated herein by
reference) .
1 0 In one approach, the three-dimensional structure of a protein of interest, or of a
protein-inhibitor complex, is determined by x-ray crystallography, by computer modeling or,
most typically, by a combination of the two approaches. Both the shape and charges of the
polypeptide must be ascertained to elucidate the structure and to determine active site(s) of the
molecule. Less often, useful information regarding the structure of a polypeptide is gained by
1 5 modeling based on the structure of homologous proteins. In both cases, relevant structural
information is used to design efficient inhibitors. Useful examples of rational drug design
include molecules which have improved activity or stability as shown by Braxton S and Wells
JA (1992 Biochemistry 31:7796-7801) or which act as inhibitors, agonists, or antagonists
of native peptides as shown by Athauda SB et al (1993 J Biochem 113:742-746), incorporated
herein by reference.
It is also possible to isolate a target-specific antibody, selected by functional assay, as
described above, and then to solve its crystal structure. This approach, in principle, yields a
pharmacore upon which subsequent drug design is based. It is possible to bypass protein
crystallography altogether by generating anti-idiotypic antibodies (anti-ids) to a functional,
pharmacologically active antibody. As a mirror image of a mirror image, the binding site of the
anti-ids is expected to be an analog of the original receptor. The anti-id is then used to identify
and isolate peptides from banks of chemically or biologically produced peptides. The isolated
peptides then act as the pharmacore.
By virtue of the present invention, sufficient amount of polypeptide is made available to
perform such analytical studies as X-ray crystallography. In addition, knowledge of the SMAP
amino acid sequence provided herein provides guidance to those employing computer modeling
techniques in place of or in addition to x-ray crystallography.
XIV Identification of Other Members of the Signal Transduction Complex
The inventive purified SMAP is a research tool for identification, characterization and
8 7 2 ~
WO 97/02347 PCT/US96tlll70
purification of interacting or signal transduction pathway proteins. Radioactive labels are
incorporated into SMAP by various methods known in the art and used to capture either soluble
or membrane-bound molecules. A preferred method involves labeling the primary amino
groups in SMAP with 1251 Bolton-Hunter reagent (Bolton, AE and Hunter, WM (1973) Biochem
J 133: 529~. This reagent has been used to label various molecules without concomitant loss of
biological activity (Hebert CA et al (1991) J Biol Chem 266: 18989; McColl S et al (1993) J
Immunol 150:4550-4555). Membrane-bound molecules are incubated with the labeled SMAP
molecules, washed to removed unbound molecules, and the SMAP complex is quantified. Data
obtained using different concentrations of SMAP are used to c~lclJ~te values for the number,
1 o affinity, and association of SMAP complex.
Labeled SMAP is also useful as a reagent for the purification of molecules with which
SMAP interacts. In one embodiment of affinity purification, SMAP is covalently coupled to a
chromatography column. Cells and their membranes are extracted, SMAP is removed and
various SMAP-free subcomponents are passed over the column. Molecules bind to the column
1 5 by virtue of their SMAP affinity. The SMAP-complex is recovered from the column, dissociated
and the recovered molecule is subjected to N-terminal protein sequencing. This amino acid
sequence is then used to identify the captured molecule or to design degenerate oligonucleotide
probes for cloning its gene from an appropriate cDNA library.
In another alternate method, antibodies are raised against SMAP, specifically monoclonal
antibodies. The monoclonal antibodies are screened to identify those which inhibit the binding of
labeled SMAP. These monoclonal antibodies are then used in affinity purification or expression
cloning of ~soci~ted molecules.
Other soluble binding molecules are identified in a similar manner. Labeled SMAP is
incubated with extracts or other appropriate materials derived from stomach or other
gastrointestinal mucosa. After incuh~tion, SMAP complexes (which are larger than the lone
SMAP molecule) are identified by a sizing technique such as size exclusion chromatography or
density gradient centrifugation and are purified by methods known in the art. The soluble
binding protein(s) are subjected to N-terminal sequencing to obtain information sufficient for
database identification, if the soluble protein is known, or for cloning, if the soluble protein is
unknown.
XV Use and Administration of Antibodies, Inhibitors, Receptors or
Antagonists of SMAP
Antibodies, inhibitors, receptors or antagonists of SMAP (or other treatments to limit
signal transduction, TST) provide different effects when administered therapeutically. TSTs
0~ ~ 98 729
WO 97/02347 PCT/US96/11170
are formulated in a nontoxic, inert, pharmaceutically acceptable aqueous carrier medium
preferably at a pH of about 5 to 8, more preferably 6 to 8, although the pH may vary accordi.,g
to the characteristics of the antibody, inhibitor, or antagonist being formulated and the
condition to be treated. Characteristics of TSTs include solubility of the molecule, half-life and
antigenicity/immunogenicity; these and other characteristics aid in defining an effective
carrier. Native human proteins are preferred as TSTs, but organic or synthetic molecules
resulting from drug screens are equally effective in particular situations.
TSTs are delivered by known routes of administration including but not limited to topical
creams and gels; transmucosal spray and aerosol; transdermal patch and bandage; injectable,
0 intravenous and lavage formulations; and orally administered liquids and pills particularly
formulated to resist stomach acid and enzymes. The particular formulation, exact dosage, and
route of admi"iil,~lion are determined by the attending physician and vary according to each
specific situation.
Such determinations are made by considering multiple variables such as the condition to
be treated, the TST to be administered, and the pharmacokinetic profile of the particular TST.
Additional factors which are taken into account include disease state (e.g. severity) of the
patient, age, weight, gender, diet, time and frequency of adminisl,alion, drug co",bi,)ation,
reaction sensitivities, and tolerance/response to therapy. Long acting TST formulations might
be administered every 3 to 4 days, every week, or once every two weeks depending on half-life
and clearance rate of the particular TST.
Normal dosage amounts vary from 0.1 to 100,000 micrograms, up to a total dose ofabout 1 9, depending upon the route of adm ~i~lr~lion. Guidance as to particular dos~ges and
methods of delivery is provided in the literature. See US Patent No. 4,657,760; 5,206,344;
or 5,225,212. Those skilled in the art employ different formulations for different TSTs.
Administration to cells such as nerve cells necessi~tes delivery in a manner different from that
to other cells such as vascular endothelial cells.
It is contemplated that conditions or diseases which trigger defensive signal transduction
may precipitate damage that is treatable with TSTs. These conditions or ~ise~ces are
specifically diagnosed by the tests ~liscussed above, and such testing should be performed in
suspected cases of stomach conditions such as gastritis, ulcers, viral and bacterial infections,
or neoplasms associated with abnormal signal transduction.
All publications and patents mentioned in the above specification are herein incorporated
by reference. Various modifications and variations of the described method and system of the
invention are apparent to those skilled in the art without departing from the scope and spirit of
24
W097/02347 i 2 ~ ~ 8 7 ~ g PCT/US96/11170
the invention. Although the invention has been described in connection with specific preferred
embodiments, it should be understood that the invention as claimed should not be unduly limited
to such specific embodiments. Indeed, various modi~ications of the above-described modes for
carrying out the invention which are obvious to those skilled in the field of molecular biology or
related fields are intended to be within the scope of the following claims.
W O 97/02347 2 ~ 9 8 7 ~ 9 PCT~US96/11170
PF-0036 PCT
SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: INCYTE PHARMACEUTICALS, INC.
(ii) TITLE OF INVENTION: A NOVEL HUMAN MAP KINASE HOMOLOG
(iii) NUMBER OF SEQUENCES: 6
(iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: INCYTE PHARMACEUTICALS, INC.
(B) STREET: 3174 Porter Drive
(C) CITY: Palo Alto
(D) STATE: CA
(E) COUNTRY: USA
(F) ZIP: 94304
(v) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: Floppy disk
(B) COMPUTER: IBM PC compatible
(C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: FastSEQ Version 1.5
(vi) CURRENT APPLICATION DATA:
(A) PCT APPLICATION NUMBER: TO BE ASSIGNED
(B) FILING DATE: 28-JUN-1996
(C) CLASSIFICATION:
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION SERIAL NO:60/000,722
(B) FILING DATE: 30-JUN-1995
(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: Billings, Lucy J.
(B) REGISTRATION NUMBER: 36,749
(C) REFERENCE/DOC~ET NUMBER: PF-0036 PCT
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPHONE: 415-855-0555
(B) TELEFAX: 415-845-4166
(2) INFORMATION FOR SEQ ID NO:1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1851 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA
(vii) IMMEDIATE SOURCE:
(A) LIBRARY: Stomach
(B) CLONE: 214915
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:
GCCCGTTGGG CCGCGAACGC AGCCGCCACG CCGGGGCCGC CGAGATCGGG TGCCCGGGAT 60
26
W 0 97/02347 ~ 8 7 ~ ~ PCT~US96/11170
PF-0036 PCT
GAGCCTCATC CGGAAAAAGG GCTTCTACAA GCAGGACGTC AACAAGACCG CCTGGGAGCT 120
GCCCAAGACC TACGTGTCCC CGACGCACGT CGGCAGCGGG GCCTATGGCT CCGTGTGCTC 180
GGCCATCGAC AAGCGGTCAG GGGAGAAGGT GGCCATCAAG AAGCTGAGCC GACCCTTTCA 240
GTCCGAGATC TTCGCCAAGC GCGCCTACCG GGAGCTGCTG TTGCTGAAGC ACATGCAGCA 300
TGAGAACGTC ATTGGGCTCC TGGATGTCTT CACCCCAGCC TCCTCCCTGG AACTTCTATG 360
ACTTCTACCT GGTGATGCCC TTCATGCAGA CGGATCTGCA GAAGATCATG GGGATGGAGT q20
TCAGTGAGGA GAAGATCCAG TACCTGGTGT ATCAGATGCT CAAAGGCCTT AAGTACATCC 480
ACTCTGCTGG GGTCGTGCAC AGGGACCTGA AGCCAGGCAA CCTGGCTGTG AATGAGGACT 540
GTGAACTGAA GATTCTGGAT TTGGGGCTGG CGCGACATGC AGACGCCGAG ATGACTGGCT 600
ACGTGGTGAC CCGCTGGTAC CGAGCCCCCG AGGTGATCCT CAGCTGGATG CACTACAACC 660
AGACAGTGGA CATCTGGTCT GTGGGCTGTA TCATGGCAGA GATGCTGACA GGGAAAACTC 720
TGTTCAAGGG GAAAGATTAC CTGGACCAGC TGACCCAGAT CCTGAAAGTG ACCGGGGTGC 780
CTGGCACGGA GTTTGTGCAG AAGCTGAACG ACAAAGCGGC CAAATCCTAC ATCCAGTCCC 840
TGCCACAGAC CCCCAGGAAG GATTTCACTC AGCTGTTCCC ACGGGCCAGC CCCCAGCCTG 900
CGGACCTGCT GGAGAAGATG CTGGAGCTAG ACGTGGACAA GCGCCTGACG GCCGCGCAGG 960
CCCTCACCCA TCCCTTCTTT GAACCCTTCC GGGACCCTGA GGAAGAGACG GAGGCCCAGC 1020
AGCCGTTTGA TGATTCCTTA GAACACGAGA AACTCACAGT GGATGAATGG AAGCAGCACA 1080
TCTACAAGGA GATTGTGAAC TTCAGCCCCA TTGCCCGGAA GGACTCACGG CGCCGGAGTG 1140
GCATGAAGCT GTAGGGACTC ATCTTGCATG GCACCGCCGG CCAGACACTG CCCAAGGACC 1200
AGTATTTGTC ACTACCAAAC TCAGCCCTTC TTGGAATACA GCCTTTCAAG CAGAGGACAG 1260
AAGGGTCCTT CTCCTTATGT GGGAAATGGG CCTAGTAGAT GCAGAATTCA AAGATGTCGG 1320
TTGGGAGAAA CTAGCTCTGA TCCTAACAGG CCACGTTAAA CTGCCCATCT GGAGAATCGC 1380
CTGCAGGTGG GGCCCTTTCC TTCCCGCCAG AGTGGGGCTG AGTGGGCGCT GAGCCAGGCC 1440
GGGGGCCTAT GGCAGTGATG CTGTGTTGGT TTCCTAGGGA TGCTCTAACG AATTACCACA 1500
AACCTGGTGG ATTGAAACAG CAGAACTTGA TTCCCTTACA GTTCTGGAGG CTGGAAATCT 1560
GGGATGGAGG TGTTGGCAGG GCTGTGGTCC CTTTGAAGGC TCTGGGGAAG AATCCTTCCT 1620
TGGCTCTTTT TAGCTTGTGG CGGCAGTGGG CAGTCCGTGG CATTCCCCAG CTTATTGCTG 1680
CATCACTCCA GTCTCTGTCT CTTCTGTTCT CTCCTCTTTT AACAACAGTC ATTGGATTTA 1740
GGGCCCACCC TAATCCTGTG TGATCTTATC TTGATCCTTA TTAATTAAAC CTGCAAATAC 1800
TCTAGTTCCA AATAAAGTCA CATTCTCAGG TAAPAAAAAA ~AAAAAAAAA A 1851
(2) INFORMATION FOR SEQ ID NO:2:
W 0 97/02347 2 ~ 9 8 7 2 9 PCT~USg6/11170
PF-0036 PCT
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 365 amino aclds
(B) TYPE: amlno acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(vii) IMMEDIATE SOURCE:
(A) LIBRARY: Stomach
(B) CLONE: 214915
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:
Met Ser Leu Ile Arg Lys Lys Gly Phe Tyr Lys Gln Asp Val Asn Lys
1 5 10 15
hr Ala Trp Glu Leu Pro Lys Thr Tyr Val Ser Pro Thr His Val Gly
Ser Gly Ala Tyr Gly Ser Val Cys Ser Ala Ile Asp Lys Arg Ser Gly
Glu Lys Val Ala Ile Lys Lys Leu Ser Arg Pro Phe Gln Ser Glu Ile
Phe Ala Lys Arg Ala Tyr Arg Glu Leu Leu Leu Leu Lys His Met Gln
is Glu Asn Val Ile Gly Leu Leu Asp Val Phe Thr Pro Ala Ser Ser
eu Gly Asn Phe Tyr Asp Phe Tyr Leu Val Met Pro Phe Met Gln Thr
100 105 110
Asp Leu Gln Lys Ile Met Gly Met Glu Phe Ser Glu Glu Lys Ile Gln
115 120 125
Tyr Leu Val Tyr Gln Met Leu Lys Gly Leu Lys Tyr Ile His Ser Ala
130 135 140
Gly Val Val His Arg Asp Leu Lys Pro Gly Asn Leu Ala Val Asn Glu
145 150 155 160
sp Cys Glu Leu Lys Ile Leu Asp Leu Gly Leu Ala Arg His Ala Asp
165 170 175
la Glu Met Thr Gly Tyr Val Val Thr Arg Trp Tyr Arg Ala Pro Glu
180 185 190
Val Ile Leu Ser Trp Met His Tyr Asn Gln Thr Val Asp Ile Trp Ser
195 200 205
Val Gly Cys Ile Met Ala Glu Met Leu Thr Gly Lys Thr Leu Phe Lys
210 215 220
Gly Lys Asp Tyr Leu Asp Gln Leu Thr Gln Ile Leu Lys Val Thr Gly
225 230 235 240
al Pro Gly Thr Glu Phe Val Gln Lys Leu Asn Asp Lys Ala Ala Lys
245 250 255
28
W 0 97/02347 PCT~US96/11170
PF-0036 PCT
er Tyr Ile Gln Ser Leu Pro Gln Thr Pro Arg Lys Asp Phe Thr Gln
260 265 270
Leu Phe Pro Arg Ala Ser Pro Gln Pro Ala Asp Leu Leu Glu Lys Met
275 280 285
Leu Glu Leu Asp Val Asp Lys Arg Leu Thr Ala Ala Gln Ala Leu Thr
290 295 300
His Pro Phe Phe Glu Pro Phe Arg Asp Pro Glu Glu Glu Thr Glu Ala
305 310 315 320
ln Gln Pro Phe Asp Asp Ser Leu Glu His Glu Lys Leu Thr Val Asp
325 330 335
lu Trp Lys Gln His Ile Tyr Lys Glu Ile Val Asn Phe Ser Pro Ile
340 345 350
la Arg Lys Asp Ser Arg Arg Arg Ser Gly Met Lys Leu
355 360 365
(2) INFORMATION FOR SEQ ID NO:3:
~i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 360 amino acids
(B) TYPE: amino acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
~ii) MOLECULE TYPE: peptide
(vii) IMMEDIATE SOURCE:
(A) LIBRARY:GenBank
(B) CLONE: GI 531125
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:
Met Ser Gln Glu Arg Pro Thr Phe Tyr Arg Gln Glu Leu Asn Lys Thr
1 5 10 15
Ile Trp Glu Val Pro Glu Arg Tyr Gln Asn Leu Ser Pro Val Gly Ser
Gly Ala Tyr Gly Ser Val Cys Ala Ala Phe Asp Thr Lys Thr Gly His
g0 45
Arg Val Ala Val Lys Lys Leu Ser Arg Pro Phe Gln Ser Ile Ile His
Ala Lys Arg Thr Tyr Arg Glu Leu Arg Leu Leu Lys His Met Lys His
Glu Asn Val Ile Gly Leu Leu Asp Val Phe Thr Pro Ala Arg Ser Leu
Glu Glu Phe Asn Asp Val Tyr Leu Val Thr His Leu Met Gly Ala Asp
100 105 110
Leu Asn Asn Ile Val Lys Cys Gln Lys Leu Thr Asp Asp His Val Gln
115 120 125
Phe Leu Ile Tyr Gln Ile Leu Arg Gly Leu Lys Tyr Ile His Ser Ala
130 135 140
Asp Ile Ile His Arg Asp Leu Lys Pro Ser Asn Leu Ala Val Asn Glu
145 150 155 160
Asp Cys Glu Leu Lys Ile Leu Asp Phe Gly Leu Ala Arg His Thr Asp
165 170 175
Asp Glu Met Thr Gly Tyr Val Ala Thr Arg Trp Tyr Arg Ala Pro Glu
W 0 97/02347 2 9 9 8 7 2 9 PCTAUS96/11170
PF-0036 PCT
180 185 190
Ile Met Leu Asn Trp Met His Tyr Asn Gln Thr Val Asp Ile Trp Ser
195 200 205
Val Gly Cys Ile Met Ala Glu Leu Leu Thr Gly Arg Thr Leu Phe Pro
210 215 220
Gly Thr Asp His Ile Asp Gln Leu Lys Leu Ile Leu Arg Leu Val Gly
225 230 235 240
Thr Pro Gly Ala Glu Leu Leu Lys Lys Ile Ser Ser Glu Ser Ala Arg
245 250 255
Asn Tyr Ile Gln Ser Leu Ala Gln Met Pro Lys Met Asn Phe Ala Asn
260 265 270
Val Phe Ile Gly Ala Asn Pro Leu Ala Val Asp Leu Leu Glu Lys Met
275 280 285
Leu Val Leu Asp Ser Asp Lys Arg Ile Thr Ala Ala Gln Ala Leu Ala
290 295 300
His Ala Tyr Phe Ala Gln Tyr His Asp Pro Asp Asp Glu Pro Val Ala
305 310 315 320
Asp Pro Tyr Asp Gln Ser Phe Glu Ser Arg Asp Leu Leu Ile Asp Glu
325 330 335
Trp Lys Ser Leu Thr Tyr Asp Glu Val Ile Ser Phe Val Pro Pro Pro
340 345 350
Leu Asp Gln Glu Glu Met Glu Ser
355 360
(2) INFORMATION FOR SEQ ID NO:4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 360 amino acids
(B) TYPE: amino acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: peptide
(vii) IMMEDIATE SOURCE:
(A) LIBRARY: Oligomer R
(B) CLONE:
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:
Met Ser Gln Glu Arg Pro Thr Phe Tyr Arg Gln Glu Leu Asn Lys Thr
1 5 10 15
Ile Trp Glu Val Pro Glu Arg Tyr Gln Asn Leu Ser Pro Val Gly Ser
Gly Ala Tyr Gly Ser Val Cys Ala Ala Phe Asp Thr Lys Thr Gly Leu
Arg Val Ala Val Lys Lys Leu Ser Arg Pro Phe Gln Ser Ile Ile His
Ala Lys Arg Thr Tyr Arg Glu Leu Arg Leu Leu Lys His Met Lys His
Glu Asn Val Ile Gly Leu Leu Asp Val Phe Thr Pro Ala Arg Ser Leu
Glu Glu Phe Asn Asp Val Tyr Leu Val Thr His Leu Met Gly Ala Asp
100 105 110
Leu Asn Asn Ile Val Lys Cys Gln Lys Leu Thr Asp Asp His Val Gln
115 120 125
Phe Leu Ile Tyr Gln Ile Leu Arg Gly Leu Lys Tyr Ile His Ser Ala
130 135 140
Asp Ile Ile His Arg Asp Leu Lys Pro Ser Asn Leu Ala Val Asn Glu
145 150 155 160
Asp Cys Glu Leu Lys Ile Leu Asp Phe Gly Leu Ala Arg His Thr Asp
7 ~ ~
W 0 97/02347 PCTrUS96/11170
PF-0036 PCT
165 170 17Asp Glu Met Thr Gly Tyr Val Ala Thr Arg Trp Tyr Arg Ala Pro Glu
180 185 190
Ile Met Leu Asn Trp Met His Tyr Asn Gln Thr Val Asp Ile Trp Ser
195 200 205
Val Gly Cys Ile Met Ala Glu Leu Leu Thr Gly Arg Thr Leu Phe Pro
210 215 220
Gly Thr Asp His Ile Asn Gln Leu Gln Gln Ile Met Arg Leu Thr Gly
225 230 235 240
Thr Pro Pro Ala Tyr Leu Ile Asn Arg Met Pro Ser His Glu Ala Arg
245 250 255
Asn Tyr Ile Gln Ser Leu Thr Gln Met Pro Lys Met Asn Phe Ala Asn
260 265 270
Val Phe Ile Gly Ala Asn Pro Leu Ala Val Asp Leu Leu Glu Lys Met
275 280 285
Leu Val Leu Asp Ser Asp Lys Arg Ile Thr Ala Ala Gln Ala Leu Ala
290 295 300
His Ala Tyr Phe Ala Gln Tyr His Asp Pro Asp Asp Glu Pro Val Ala
305 310 315 320
Asp Pro Tyr Asp Gln Ser Phe Glu Ser Arg Asp Leu Leu Ile Asp Glu
325 330 335
Trp Lys Ser Leu Thr Tyr Asp Glu Val Ile Ser Phe Val Pro Pro Pro
340 345 350
Leu Asp Gln Glu Glu Met Glu Ser
355 360
(2) INFORMATION FOR SEQ ID NO:5:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA
(vii) IMMEDIATE SOURCE:
(A) LIBRARY: Oligomer F
(B) CLONE:
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:
AAGACATCCA GGAGCCCAAT G 21
(2) INFORMATION FOR SEQ ID NO:6:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA
(vii) IMMEDIATE SOURCE:
(A) LIBRARY: GenBank
(B) CLONE: GI 603917
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:
AGGTGATCCT CAGCTGGATG CAC 23
