U.S. patent application number 14/479637 was filed with the patent office on 2015-05-14 for monomeric forms of human aminoacyl-trna synthetases having non-canonical biological activities.
The applicant listed for this patent is THE SCRIPPS RESEARCH INSTITUTE. Invention is credited to Paul Schimmel, Bonnie Slike, Xiang-Lei Yang.
Application Number | 20150132277 14/479637 |
Document ID | / |
Family ID | 44356032 |
Filed Date | 2015-05-14 |
United States Patent
Application |
20150132277 |
Kind Code |
A1 |
Schimmel; Paul ; et
al. |
May 14, 2015 |
Monomeric Forms of Human Aminoacyl-tRNA Synthetases Having
Non-Canonical Biological Activities
Abstract
Isolated monomeric aminoacyl-tRNA synthetase polypeptides and
polynucleotides having non-canonical biological activities are
provided, as well as compositions and methods related thereto.
Inventors: |
Schimmel; Paul; (La Jolla,
CA) ; Yang; Xiang-Lei; (San Diego, CA) ;
Slike; Bonnie; (Ellicott City, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE SCRIPPS RESEARCH INSTITUTE |
LA JOLLA |
CA |
US |
|
|
Family ID: |
44356032 |
Appl. No.: |
14/479637 |
Filed: |
October 9, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13577090 |
Oct 16, 2012 |
8828685 |
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PCT/US2011/000210 |
Feb 4, 2011 |
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14479637 |
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61337528 |
Feb 4, 2010 |
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Current U.S.
Class: |
424/94.5 ;
435/183; 435/350; 435/358; 435/367; 435/369; 435/375; 530/387.9;
530/389.4 |
Current CPC
Class: |
C12Y 601/01002 20130101;
C07K 16/1045 20130101; C12N 9/93 20130101; C07K 16/40 20130101;
A61K 38/45 20130101; A61P 29/00 20180101; C12Y 601/01 20130101;
C12Y 601/01001 20130101; C12Y 601/01006 20130101; Y02A 50/473
20180101 |
Class at
Publication: |
424/94.5 ;
435/183; 530/389.4; 435/375; 435/358; 435/367; 435/350; 435/369;
530/387.9 |
International
Class: |
C12N 9/00 20060101
C12N009/00; C07K 16/40 20060101 C07K016/40; C07K 16/10 20060101
C07K016/10 |
Goverment Interests
STATEMENT OF GOVERNMENT SUPPORT
[0002] This invention was made with government support under Grant
Nos. CA092577, GM015539 and RR025204 awarded by the National
Institutes of Health. The U.S. Government has certain rights in the
invention.
Claims
1. An isolated aminoacyl-tRNA (AARS) synthetase polypeptide having
a non-canonical biological activity, or an active fragment or
variant thereof, wherein the polypeptide is substantially in a
monomeric form under physiological conditions or in solution.
2. The isolated polypeptide of claim 1, wherein the polypeptide
comprises one or more stabilizing modifications in relation to a
wild-type AARS sequence that reduce its ability to dimerize with
itself or another AARS polypeptide.
3. The isolated polypeptide of claim 2, wherein the one or more
modifications are selected from amino acid substitution(s), amino
acid deletion(s), amino acid addition(s)/insertion(s),
truncation(s), and chemical modification(s).
4. The isolated polypeptide of claim 2, comprising one or more
stabilizing modifications located within or proximal to the
primary, secondary, or tertiary structure of the dimer
interface.
5. The isolated polypeptide of claim 2, wherein the one or more
stabilizing modifications are proximal to the primary structure of
the dimer interface by about 1-20 residues.
6. The isolated polypeptide of any one of claims 1-5, wherein the
polypeptide is a substantially monomeric form of tyrosyl-tRNA
synthetase (YRS), tryptophanyl-tRNA synthetase (WRS), lysyl-tRNA
synthetase (KRS), glutaminyl-tRNA synthetase (QRS), glycyl-tRNA
synthetase (GlyRS), histidyl-tRNA synthetase (HisRS), seryl-tRNA
synthetase (SRS), phenyl alanyl-tRNA synthetase (PheRS),
alanyl-tRNA synthetase (AlaRS), asparaginyl-tRNA synthetase
(AsnRS), aspartyl-tRNA synthetase (AspRS), cysteinyl-tRNA
synthetase (CysRS), glutamyl-tRNA synthetase (ERS), prolyl-tRNA
synthetase (ProRS), arginyl-tRNA synthetase (RRS), isoleucyl-tRNA
synthetase (IRS), leucyl-tRNA synthetase (LRS), threonyl-tRNA
synthetase (TRS), methionyl-tRNA synthetases (MRS), or valyl-tRNA
synthetase (VRS).
7. The isolated polypeptide of claim 6, wherein the polypeptide is
a tyrosyl-tRNA (YRS) synthetase polypeptide.
8. The isolated polypeptide of claim 7, comprising one or more
stabilizing modifications of Pro 159, Leu 160, or Leu 161, or any
combination thereof.
9-12. (canceled)
13. The isolated polypeptide of claim 6, wherein the polypeptide is
a tryptophanyl-tRNA synthetase (WRS) polypeptide.
14. The isolated polypeptide of claim 13, comprising one or more
stabilizing modifications of F260, Y201, I278, H130, or E408, or
any combination thereof.
15. The isolated polypeptide of claim 13, comprising an amino acid
sequence at least 80%, 85%, 90%, 95%, or 98% identical to SEQ ID
NO:4 or 7-9, or a biologically active fragment thereof, wherein the
polypeptide comprises a modification of F260, Y201, I278, H130, or
E408, or any combination thereof.
16. The isolated polypeptide of claim 13, comprising the amino acid
sequence of SEQ ID NO:8 or 9.
17. The isolated polypeptide of claim 6, wherein the polypeptide is
a lysyl-tRNA synthetase (KRS) polypeptide, or a truncation or
variant thereof.
18-34. (canceled)
35. A pharmaceutical composition, comprising an isolated
aminoacyl-tRNA (AARS) synthetase polypeptide according to any one
of claims 1-34, and a pharmaceutically acceptable carrier.
36. A method of modulating an inflammatory response in subject,
comprising administering to the subject an isolated aminoacyl-tRNA
(AARS) synthetase polypeptide according to any one of claims 1-34,
or a pharmaceutical composition according to claim 15.
57. A method of treating a condition, comprising administering to a
subject in need thereof an isolated aminoacyl-tRNA (AARS)
synthetase polypeptide according to any one of claims 1-34, or a
pharmaceutical composition according to claim 35, wherein the
condition is selected from the group consisting of an inflammatory
condition, an autoimmune condition, a neoplastic disease, a
metabolic disease, a neurological disease, an infection, an
immunodeficiency, a cardiovascular disease, and a condition
associated with angiogenesis.
65. A composition, comprising a human immunodeficiency virus (HIV)
Gag protein and a substantially monomeric lysyl tRNA synthetase
(KRS) polypeptide according to any one of claims 17-26, which
comprises one or more stabilizing modifications that do not
significantly reduce KRS binding to HIV Gag.
66. A modified cell, comprising a human immunodeficiency virus
(HIV) Gag protein and an exogenous, substantially monomeric lysyl
tRNA synthetase (KRS) polypeptide according to any one of claims
17-26, which comprises one or more stabilizing modifications that
do not significantly reduce KRS binding to HIV Gag.
74. A compound or binding agent that specifically binds to (a) an
H3 and/or H4 region of a human immunodeficiency virus (HIV)
Gag-CA-CTD domain, (b) an inter-domain cavity of substantially
monomeric KRS which interacts with the H3 and/or H3 region of
Gag-CA-CTD domain, or both (a) and (b), and reduces the interaction
between HIV Gag and monomeric KRS.
75-76. (canceled)
77. A method of reducing assembly of a human immunodeficiency virus
(HIV), comprising contacting an HIV-infected cell with a compound
identified by the method of any one of claims 69-73, or the
compound or binding agent according to any one of claims 74-76.
78-105. (canceled)
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 13/577,090 (filed Oct. 16, 2012, now pending),
which is a 35 USC .sctn.371 National Stage application of
International Application No. PCT/US2011/00210 (filed Feb. 4, 2011,
now expired), which claims the benefit under 35 USC .sctn.119(e) of
U.S. Provisional Patent Application No. 61/337,528 (filed Feb. 4,
2010, now expired); U.S. Provisional Patent Application No.
61/337,488 (filed Feb. 4, 2010, now expired); and U.S. Provisional
Patent Application No. 61/337,489 (filed Feb. 4, 2010, now
expired). Each of the aforementioned priority applications is
incorporated by reference in its entirety and for all purposes.
STATEMENT REGARDING SEQUENCE LISTING
[0003] The Sequence Listing associated with this application is
provided in text format in lieu of a paper copy, and is hereby
incorporated by reference into the specification. The name of the
text file containing the Sequence Listing is
120161.sub.--423PC_SEQUENCE_LISTING.txt. The text file is about 48
KB, was created on Feb. 3, 2011, and is being submitted
electronically via EFS-Web.
BACKGROUND OF THE INVENTION
[0004] 1. Field of the Invention
[0005] The present invention relates generally to monomeric forms
of aminoacyl-tRNA synthetase (AARS) polypeptides, compositions
comprising such polypeptides, and methods of using same.
[0006] 2. Description of the Related Art
[0007] Aminoacyl-tRNA synthetases, which catalyze the
aminoacylation of tRNA molecules, are essential for decoding
genetic information during the process of translation. In higher
eukaryotes, aminoacyl-tRNA synthetases associate with other
polypeptides to form supramolecular multienzyme complexes. Each of
the eukaryotic tRNA synthetases consists of a core enzyme, which is
closely related to the prokaryotic counterpart of the tRNA
synthetase, and an additional domain that is appended to the
amino-terminal or carboxyl-terminal end of the core enzyme. Human
tyrosyl-tRNA synthetase (YRS), for example, has a carboxyl-terminal
domain that is not part of prokaryotic and lower eukaryotic YRS
molecules.
[0008] Several aminoacyl-tRNA synthetases have been demonstrated to
have non-canonical functions distinct from their involvement in
translation. For example, mini-tyrosyl tRNA synthetase (mini-YRS),
the N-terminal domain of YRS which corresponds to amino acid
residues 1-364 and is cleaved by polymorphonuclear cell elastase
and plasmin, is a member of the aminoacyl tRNA synthetase "AARS"
multifunction cytokine-like proteins and peptides. In vitro,
mini-YRS has been shown to stimulate neutrophil activation and
chemotaxis, endothelial cell proliferation and migration, and is
pro-angiogenic in chick chorioallantoic membrane (CAM) and mouse
matrigel assays. Mini-YRS has an ELR motif that, like
CXC-chemokines such as IL-8, confers its chemokine and angiogenic
activities. Like other ELR-containing cytokines, mutation of this
motif inhibits mini-YRS binding and stimulation of leukocytes and
angiogenesis.
[0009] In addition, truncated forms or WRS have been demonstrated
to have angiogenic properties. In normal human cells, there are two
forms of WRS that can be detected: a major form consisting of the
full-length molecule (amino acid residues 1-471) and a minor
truncated form. The minor form is generated by the deletion of an
amino-terminal domain through alternative splicing of the pre-mRNA.
The amino-terminus of mini-WRS has been determined to be the
methionine residue at position 48 of the full-length WRS molecule.
Alternatively, truncated WRS can be generated by proteolysis. For
example, bovine WRS is highly expressed in the pancreas and is
secreted into the pancreatic juice, thus resulting in the
production of a truncated WRS molecule. Additional studies indicate
that mini-WRS inhibits VEGF-induced cell proliferation and
migration (Wakasugi et al., Proc. Natl. Acad. Sci. 99: 173-177
(2002)). In particular, a chick CAM assay shows that mini WRS
blocks angiogenic activity of VEGF. In contrast, the full-length
WRS does not inhibit angiogenesis. Thus, removal of the first 48
amino acid residues exposes the anti-angiogenic activity of WRS.
Therefore, as with YRS, certain forms of WRS possess activities
other than the aminoacylation of tRNA.
[0010] Given these observations of non-canonical and
therapeutically relevant activities associated alternative forms of
YRS and WRS, there is a need to identify biologically relevant
forms and/or activities of other aminoacyl-tRNA synthetase proteins
in order to exploit the full therapeutic potential of this family
of proteins. Accordingly, the present invention addresses these
needs and offers other related advantages.
SUMMARY OF THE INVENTION
[0011] The present invention stems from the unexpected discovery
that dissociated monomeric forms of aminoacyl-tRNA synthetase
(AARS) polypeptides possess non-canonical biological activities of
therapeutic relevance. In certain aspects, these monomeric forms of
AARS polypeptides possess an activity that differs from that of the
dimeric form, either by degree or type. Without being bound by any
one theory, the dissociated monomer form of certain AARS
polypeptides appears to be responsible for many of their
non-canonical biological activities, and thus provides a new
mechanism for understanding how new surfaces can be exploited to
expand the functions of AARS polypeptides. It is also believed that
this new paradigm is more generally applicable to understanding the
alternative and therapeutically-adaptable functions of tRNA
synthetases.
[0012] Therefore, according to one aspect, the present invention
provides isolated and substantially monomeric AARS polypeptides
having at least one non-canonical biological activity, as well
active fragments and variants thereof which substantially retain
said non-canonical activity. "Non-canonical" activity," as used
herein, refers generally to an activity possessed by an AARS
polypeptide of the invention that is other than aminoacylation and,
more specifically, other than the addition of its cognate amino
acid onto a tRNA molecule.
[0013] As detailed herein, in certain embodiments, a non-canonical
biological activity exhibited by a monomeric AARS polypeptide of
the invention may include, but is not limited to, modulation of
cell proliferation, modulation of cell differentiation, modulation
of apoptosis, modulation of cell signaling, modulation of
angiogenesis (e.g., via VE-cadherin), modulation of cell migration,
modulation of cell binding, modulation of cellular metabolism,
modulation of cytokine production or activity, modulation of
cytokine receptor activity (e.g., CXCR-1, CXCR-2), and the like. In
certain embodiments, a non-canonical biological activity includes
inhibiting or reducing angiogenesis, i.e., an angiostatic activity.
In certain embodiments, monomeric AARS (e.g., YRS) polypeptides are
cytokine receptor agonists, such as CXCR-1 and CXCR-2 agonists. In
certain embodiments, as noted above, isolated monomeric AARS
polypeptides possess non-canonical biological activities, such as
angiostatic activities, cytokine receptor-agonist activities,
and/or cadherin-modulatory activities, which are not possessed by
dimeric AARS polypeptide complexes, or which contrast the activity
of a dimeric AARS.
[0014] Certain embodiments therefore include isolated
aminoacyl-tRNA (AARS) synthetase polypeptides having a
non-canonical biological activity, or active fragment or variant
thereof, wherein the polypeptide is substantially in a monomeric
form under physiological conditions or in solution. In certain
embodiments, the polypeptide comprises one or more stabilizing
modifications in relation to a wild-type sequence that reduce its
ability to dimerize with itself or with another AARS
polypeptide.
[0015] In certain embodiments, the one or more modifications are
selected from any one or more of amino acid substitutions, amino
acid deletions, amino acid additions, truncations, and chemical
modifications. Certain embodiments include one or more stabilizing
modifications located within or proximal to the primary, secondary,
or tertiary structure of the dimer interface. In certain
embodiments, the one or more stabilizing modifications are proximal
to the primary structure of the dimer interface by about 1-20
residues.
[0016] In certain embodiments, the AARS polypeptide is a
tyrosyl-tRNA synthetase (YRS), a tryptophanyl-tRNA synthetase
(WRS), a glutaminyl-tRNA synthetase (QRS), a glycyl-tRNA synthetase
(GlyRS), a histidyl-tRNA synthetase (HisRS), a seryl-tRNA
synthetase (SRS), a phenylalanyl-tRNA synthetase (PheRS), an
alanyl-tRNA synthetase (AlaRS), an asparaginyl-tRNA synthetase
(AsnRS), an aspartyl-tRNA synthetase (AspRS), a cysteinyl-tRNA
synthetase (CysRS), a glutamyl-tRNA synthetase (ERS), a prolyl-tRNA
synthetase (ProRS), an arginyl-tRNA synthetase (RRS), an
isoleucyl-tRNA synthetase (IRS), a leucyl-tRNA synthetase (LRS), a
lysyl-tRNA synthetase (KRS), a threonyl-tRNA synthetase (TRS), a
methionyl-tRNA synthetases (MRS), or a valyl-tRNA synthetase
(VRS).
[0017] In certain embodiments, the monomeric form has an increased
non-canonical biological activity as compared to a dimeric form of
the polypeptide. In certain embodiments, the monomeric form has a
different non-canonical biological activity as compared to a
dimeric form of the polypeptide. In certain embodiments, the
non-canonical biological activity comprises a cytokine receptor
agonist activity or a cadherin-modulatory activity. In certain
embodiments, the cytokine receptor is CXCR-1, CXCR-2, or both. In
certain embodiments, the cytokine receptor agonist activity
modulates an inflammatory response or modulates an angiogenic
response. In certain embodiments, the cytokine receptor agonist
activity increases an inflammatory response or increases an
angiogenic response. In certain embodiments, the inflammatory or
angiogenic response comprises increased endothelial cell or
polymorphonuclear cell (PMNC) migration or proliferation. In
certain embodiments, the cadherin modulatory activity comprises a
VE-cadherin inhibitory activity. In certain embodiments, the
VE-cadherin inhibitory activity reduces angiogenesis.
[0018] Certain embodiments include a substantially monomeric
aminoacyl-tRNA (AARS) synthetase polypeptide as described herein,
and a pharmaceutically acceptable carrier. Certain embodiments
relate to methods of modulating an inflammatory response in a
subject, comprising administering to the subject a substantially
monomeric aminoacyl-tRNA (AARS) synthetase polypeptide described
herein. Certain embodiments include increasing the inflammatory
response in the subject. Certain embodiments include reducing or
maintaining the inflammatory response in the subject.
[0019] Certain embodiments relate to methods of modulating
angiogenesis in a subject, comprising administering to the subject
a substantially monomeric aminoacyl-tRNA (AARS) synthetase
polypeptide described herein. Certain embodiments include
increasing angiogenesis in the subject. Certain embodiments include
reducing angiogenesis in the subject.
[0020] Certain embodiments include methods of modulating the levels
or activity of CXCR-1 or CXCR-2 in a cell, comprising contacting
the cell with substantially monomeric aminoacyl-tRNA synthetase
(AARS) polypeptide. Certain embodiments include increasing the
levels or activity of CXCR-1 or CXCR-2 in the cell. In certain
embodiments, the cell is in a subject. Certain embodiments include
increasing endothelial cell or polymorphonuclear cell (PMNC)
migration or proliferation.
[0021] Certain embodiments include methods of modulating the
levels, phosphorylation state, or a biological activity of
VE-cadherin in a cell, comprising contacting the cell with
substantially monomeric aminoacyl-tRNA synthetase (AARS)
polypeptide. Certain embodiments include reducing the levels of
VE-cadherin in the cell. In certain embodiments, the cell is in a
subject. Certain embodiments include reducing the levels of
circulating VE-cadherin in the subject. Certain embodiments include
reducing the phosphorylation of VE-cadherin at one or more tyrosine
residues. Certain embodiments include reducing the biological
activity of VE-cadherin. In certain embodiments, the biological
activity comprises the ability to associate with, or promote the
signaling of, vascular endothelial cell growth factor receptor
(VEGFR2). In certain embodiments, the biological activity comprises
the ability of one or more VE-cadherin polypeptides to
self-assemble, or to associate with other VE-cadherin
polypeptides.
[0022] Certain embodiments include directly binding to VE-cadherin
and thereby reducing the biological activity of VE-cadherin. In
certain embodiments, the biological activity comprises the ability
to associate with, or promote the signaling of, vascular
endothelial cell growth factor receptor (VEGFR2). In certain
embodiments, the biological activity comprises the ability of one
or more VE-cadherin polypeptides to self-assemble, or to associate
with other VE-cadherin polypeptides.
[0023] Certain embodiments relate to methods of treating a
condition comprising administering to a subject in need thereof
substantially monomeric aminoacyl-tRNA (AARS) synthetase
polypeptide according as described herein, wherein the condition is
selected from an inflammatory condition, an autoimmune condition, a
neoplastic disease, a metabolic disease, a neurological disease, an
infection, an immunodeficiency, a cardiovascular disease, and a
condition associated angiogenesis.
[0024] In certain embodiments, the inflammatory condition is
associated with reduced inflammation. In certain embodiments, the
condition is associated with increased inflammation. In certain
embodiments, the condition is associated with reduced angiogenesis.
In certain embodiments, the condition is associated with increased
or aberrant angiogenesis.
[0025] Specific embodiments include isolated tyrosyl-tRNA (YRS)
synthetase polypeptides having a non-canonical biological activity,
or active fragment or variant thereof, wherein the polypeptide is
substantially in a monomeric form under physiological conditions or
in solution. In certain embodiments, the YRS polypeptide comprises
one or more stabilizing modifications in relation to the wild-type
sequence such as SEQ ID NO:1 that reduce its ability to dimerize
with another YRS polypeptide. In particular embodiments, the one or
more stabilizing modifications comprises a modification of Pro 159,
Leu 160, or Leu 161, or any combination thereof. In certain
embodiments, the one or more stabilizing modifications is proximal
to residues 159-161 in the primary, secondary, or tertiary
structure of the polypeptide.
[0026] In certain embodiments, the YRS monomer polypeptide
comprises an amino acid sequence at least 80%, 85%, 90%, 95%, 98%,
or 100% identical to SEQ ID NO:1 or 3-4, or a biologically active
fragment thereof, wherein the one or more stabilizing modifications
comprises a modification of Pro 159, Leu 160, or Leu 161, or any
combination thereof. In certain embodiments, the polypeptide an
amino acid sequence at least 80%, 85%, 90%, 95%, 98%, or 100%
identical to SEQ ID NO:1 or 3-4, or a biologically active fragment
thereof, wherein the one or more stabilizing modifications is
proximal to residues 159-161 in the primary, secondary, or tertiary
structure of the polypeptide. In certain embodiments, the
polypeptide comprises an amino acid sequence at least 80%, 85%,
90%, 95%, 98%, or 100% identical to SEQ ID NO:4, and which retains
a deletion of Pro 159, Leu 160, and Leu 161 (.DELTA.159-161).
[0027] In certain embodiments, the monomeric form has an increased
or a different non-canonical biological activity as compared to a
dimeric form of a YRS polypeptide. In certain embodiments, the
non-canonical biological activity comprises a cytokine receptor
agonist activity. In certain embodiments, the cytokine receptor is
CXCR-1, CXCR-2, or both. In certain embodiments, the cytokine
receptor agonist activity modulates an inflammatory response or
modulates an angiogenic response. In certain embodiments, the
cytokine receptor agonist activity increases an inflammatory
response or increases an angiogenic response. In certain
embodiments, the inflammatory or angiogenic response comprises
increased endothelial cell or polymorphonuclear cell (PMNC)
migration or proliferation.
[0028] Certain embodiments include a substantially monomeric
tyrosyl-tRNA (YRS) synthetase polypeptide as described herein, and
a pharmaceutically acceptable carrier. Certain embodiments relate
to methods of modulating an inflammatory response in a subject,
comprising administering to the subject a substantially monomeric
tyrosyl-tRNA (YRS) synthetase polypeptide described herein. Certain
embodiments include increasing the inflammatory response in the
subject.
[0029] Certain embodiments relate to methods of modulating
angiogenesis in a subject, comprising administering to the subject
a substantially monomeric tyrosyl-tRNA (YRS) synthetase polypeptide
described herein. Certain embodiments include increasing
angiogenesis in the subject.
[0030] Certain embodiments include methods of modulating the levels
or activity of a cytokine receptor in a cell, comprising contacting
the cell with substantially monomeric tyrosyl-tRNA synthetase (YRS)
polypeptide as described herein, or a pharmaceutical composition
comprising the same. Certain embodiments relate to increasing the
levels or activity of the cytokine receptor in the cell. In certain
embodiments, the cell is in a subject. In certain embodiments, the
cytokine receptor is CXCR-1, CXCR-2, or both. In certain
embodiments, the increased activity of the cytokine receptor leads
to increased endothelial cell or PMNC migration or
proliferation.
[0031] Specific embodiments include isolated tryptophanyl-tRNA
(WRS) synthetase polypeptides having a non-canonical biological
activity, or active fragment or variant thereof, wherein the
polypeptide is substantially in a monomeric form. In certain
embodiments, the polypeptide comprises one or more stabilizing
modifications in relation to the wild-type WRS sequence such as SEQ
ID NO:5, or the T2-WRS sequence of SEQ ID NO:7, which reduce its
ability to dimerize with itself or with another WRS polypeptide. In
certain embodiments, the one or more stabilizing modifications
comprise a modification F260, Y201, I278, H130, or E408, or any
combination thereof. In certain embodiments, the monomeric WRS
polypeptide comprises SEQ ID NO:5 or 7, or a biologically active
fragment or variant thereof having 80%, 90%, 95%, or 98% sequence
identity thereto, wherein the polypeptide comprises one or more
stabilizing modifications of F260, Y201, I278, H130, or E408, or
any combination thereof. In certain embodiments, the monomeric WRS
polypeptide comprises an amino sequence at least 80%, 85%, 90%,
95%, or 98% identical to SEQ ID NO:8 or 9, which comprises one or
more stabilizing modifications of F260, Y201, I278, H130, or E408,
or any combination thereof. Certain embodiments include a
polypeptide of SEQ ID NO:8 or 9.
[0032] In certain embodiments, the WRS monomeric form has an
increased or a different non-canonical biological activity as
compared to a dimeric form of the polypeptide. In certain
embodiments, the non-canonical biological activity of the WRS
monomer comprises an angiogenesis-modulating activity. In certain
embodiments, the angiogenesis-modulating activity is an angiostatic
activity.
[0033] In certain embodiments, the WRS monomer binds directly to
VE-cadherin in a cell or on the surface of the cell. In certain
embodiments, the direct binding to VE-cadherin competitively
inhibits the interaction of VE-cadherin with one or more angiogenic
polypeptides. In certain embodiments, the one or more angiogenic
polypeptides include another VE-cadherin polypeptide. In certain
embodiments, the polypeptide disrupts VE-cadherin self-assembly in
a cell or on the surface of the cell.
[0034] Certain embodiments include a substantially monomeric
tryptophanyl-tRNA (WRS) synthetase polypeptide as described herein,
and a pharmaceutically acceptable carrier. Certain embodiments
relate to methods of modulating angiogenesis in a subject,
comprising administering to the subject a substantially monomeric
tryptophanyl-tRNA (WRS) synthetase polypeptide described herein.
Certain embodiments include reducing angiogenesis in the
subject.
[0035] Certain embodiments include methods of modulating the
levels, phosphorylation state, or a biological activity of
VE-cadherin in a cell, comprising contacting the cell with
substantially monomeric tryptophanyl-tRNA synthetase (WRS)
polypeptide as described herein, or a pharmaceutical composition
comprising the same. Certain embodiments relate to reducing the
levels of VE-cadherin in the cell. In certain embodiments, the cell
is in a host.
[0036] Certain embodiments relate to the use of WRS polypeptides to
reduce the levels of circulating VE-cadherin in the host. Certain
embodiments relate to reducing the phosphorylation of VE-cadherin
at one or more tyrosine residues.
[0037] Certain embodiments relate to WRS polypeptides that reduce
the biological activity of VE-cadherin, and related uses thereof.
In certain embodiments, the biological activity comprises the
ability to associate with, or promote the signaling of, vascular
endothelial cell growth factor receptor (VEGFR2). In certain
embodiments, the biological activity comprises the ability of one
or more VE-cadherin polypeptides to self-assemble, or to associate
with other VE-cadherin polypeptides. Certain embodiments relate to
directly binding to VE-cadherin and thereby reducing the biological
activity of VE-cadherin. In certain embodiments, the biological
activity comprises the ability to associate with, or promote the
signaling of, vascular endothelial cell growth factor receptor
(VEGFR2). In certain embodiments, the biological activity comprises
the ability of one or more VE-cadherin polypeptides to
self-assemble, or to associate with other VE-cadherin
polypeptides.
[0038] Certain embodiments relate to methods of treating a
condition comprising administering to a subject in need thereof
substantially monomeric tryptophanyl-tRNA (WRS) synthetase
polypeptide according as described herein, wherein the condition is
selected from the group consisting of inflammatory diseases,
autoimmune diseases, neoplastic diseases, metabolic diseases,
neurological diseases, infections, cardiovascular diseases, and
diseases associated with modulation of angiogenesis.
[0039] In particular embodiments, the substantially monomeric
polypeptide is a lysyl-tRNA synthetase (KRS) polypeptide, or a
truncation or variant thereof. One example of a KRS truncant is SEQ
ID NO:12. In certain embodiments, the KRS polypeptide comprises one
or more stabilizing modifications located within or proximal to the
primary, secondary, or tertiary structure of the dimer interface.
In particular embodiments, these include one or more modifications
of residues E265, 283FIT285, G310, 539YGLLP543 as defined by
full-length KRS, and/or proximal residues. In some embodiments, the
KRS polypeptide comprises one or more stabilizing modifications,
wherein said modification is a polypeptide insertion. In certain
embodiments, said insertion comprises a heterologous polypeptide
sequence. In particular embodiments, said insertion comprises one
or more of the following characteristics: (i) the polypeptide is
not derived from a membrane protein, (ii) the polypeptide has a
globular 3D structure, (iii) the polypeptide has a dimension of
about 30-40 .ANG., (iv) the N-terminus and C-terminus of the
polypeptide are located in close three-dimensional proximity, or
any combination of (i)-(iv). In specific embodiments, the insertion
comprises flavodoxin from E. coli. In preferred embodiments, the
KRS polypeptide comprises the amino acid sequence of SEQ ID
NO:13.
[0040] In certain embodiments, said insertion is inserted proximal
to or within the dimer interface of KRS. In some embodiments, said
insertion is inserted at the periphery of the dimer interface. In
specific embodiments, said insertion is inserted proximal to or at
residue G310, as defined by the full-length KRS sequence of SEQ ID
NO:11.
[0041] Also included are methods of drug discovery and related
compositions. For example, certain embodiments include compositions
(e.g., in vitro compositions), comprising a human immunodeficiency
virus (HIV) Gag protein and a substantially monomeric lysyl tRNA
synthetase (KRS) described herein, which typically or optionally
comprises one or more stabilizing modifications that do not
significantly reduce KRS binding to HIV Gag. Also included are
modified cells, comprising a human immunodeficiency virus (HIV) Gag
protein and an exogenous (e.g., recombinantly introduced),
substantially monomeric lysyl tRNA synthetase (KRS) polypeptide
described herein, which comprises one or more stabilizing
modifications that do not significantly reduce KRS binding to HIV
Gag. In some embodiments, the HIV Gag protein comprises the
Gag-CA-CTD domain. In specific embodiments, the Gag-CA-CTD domain
comprises regions H3 and H4.
[0042] Certain embodiments include methods of identifying a
compound that specifically reduces binding between a human
immunodeficiency virus (HIV) Gag protein and a substantially
monomeric lysyl tRNA synthetase (KRS) polypeptide, comprising (a)
combining the composition or cell described above with at least one
test compound under suitable conditions, and (b) detecting reduced
binding between the HIV Gag protein and the substantially monomer
KRS polypeptide, thereby identifying a compound that specifically
reduces binding between the HIV Gag protein and the KRS
polypeptide. In certain embodiments, the test compound is a
polypeptide or peptide, an antibody or antigen-binding fragment
thereof, a peptide mimetic, or a small molecule. In some
embodiments, the test compound binds to the Gag-CA-CTD domain. In
particular embodiments, the test compound binds to H3 or H4 or both
of the Gag-CA-CTD domain. In specific embodiments, the test
compound binds to the bottom side of H3 or H4 or both (see FIG.
18E).
[0043] Also included are compounds or binding agents (e.g.,
antibodies and fragments thereof) that specifically bind to (a) an
H3 and/or H4 region of a human immunodeficiency virus (HIV)
Gag-CA-CTD domain, (b) an inter-domain cavity of substantially
monomeric KRS which interacts with the H3 and/or H3 region of
Gag-CA-CTD domain, or both (a) and (b), and reduce the interaction
between HIV Gag and monomeric KRS. In certain embodiments, the
compound or binding agent binds to the bottom side of H3 or H4 or
both. In certain embodiments, the compound or binding agent mimics
the three-dimensional structure of the Gag-CA-CTD domain comprising
the H3 and/or H4 region. Certain methods include reducing assembly
of a human immunodeficiency virus (HIV), comprising contacting an
HIV-infected cell with a compound or binding described above. Such
methods, compounds, and agents can be used in the treatment of HIV
infection.
[0044] According to another aspect of the invention, there are
provided fusion proteins comprising at least one substantially
monomeric AARS polypeptide as described herein and a heterologous
fusion partner.
[0045] According to another aspect of the invention, there are
provided isolated polynucleotides encoding the polypeptides and
fusion proteins as described herein, as well as expression vectors
comprising such polynucleotides, and host cell comprising such
expression vectors.
[0046] According to yet another aspect of the invention, there are
provided compositions, e.g., pharmaceutical compositions,
comprising physiologically acceptable carriers and at least one of
the isolated polypeptides, fusion proteins, antibodies, isolated
polynucleotides, expression vectors, host cells, etc., of the
invention, as described herein.
[0047] Also provided by the present invention, in other aspects,
are methods for modulating a cellular activity by contacting a cell
or tissue with a composition of the invention, as described herein,
wherein the cellular activity to be modulated is selected from the
group consisting of cell proliferation, apoptosis, cell signaling,
cellular metabolism, angiogenesis, cell migration, cell binding,
cytokine production, cytokine receptor activity, and the like.
[0048] In other aspects, the present invention provides methods for
treating a disease, disorder or other condition in a subject in
need thereof by administering a composition according to the
present invention. By way of illustration, such diseases, disorders
or conditions may include, but are not limited to, cancer,
inflammatory disease or condition, immune disease (including
autoimmune disease) and/or conditions associated with abnormal
angiogenesis.
[0049] Also included are methods of drug discovery. For example,
certain embodiments include methods of identifying a compound that
specifically binds to a substantially monomeric aminoacyl-tRNA
synthetase (AARS) polypeptide, and/or one or more of its binding
partners (e.g., host cell, viral, bacterial binding partners),
comprising a) combining the substantially monomeric AARS
polypeptide or its binding partner or both with at least one test
compound under suitable conditions, and b) detecting binding of the
substantially monomeric AARS polypeptide or its binding partner or
both to the test compound, thereby identifying a compound that
specifically binds to the substantially monomeric AARS polypeptide
or its binding partner or both.
BRIEF DESCRIPTION OF SEQUENCE IDENTIFIERS
[0050] SEQ ID NO: 1 is the full length amino acid sequence of human
tyrosyl-tRNA synthetase (YRS).
[0051] SEQ ID NO:2 is the polynucleotide sequence that encodes
full-length human YRS.
[0052] SEQ ID NO:3 is the amino acid sequence of mini-YRS.
[0053] SEQ ID NO:4 is the amino acid sequence of the
non-associating monomeric .DELTA.159-161 variant of mini-YRS.
[0054] SEQ ID NO:5 is the full length amino acid sequence of human
tryptophanyl-tRNA synthetase (WRS).
[0055] SEQ ID NO:6 is the polynucleotide sequence that encodes
full-length human WRS.
[0056] SEQ ID NO:7 is the amino acid sequence of T2-WRS (residues
94-471 of full-length WRS).
[0057] SEQ ID NO:8 is the amino acid sequence of the
F260EY201EI278E T2-WRS variant, which forms a stable monomer.
[0058] SEQ ID NO:9 is the amino acid sequence of the
F260EY201EH130R T2-WRS variant, which forms a stable monomer.
[0059] SEQ ID NO:10 is the amino acid sequence of the VE-cadherin
extracellular domain EC1.
[0060] SEQ ID NO:11 is the full-length amino acid sequence of human
lysyl-tRNA synthetase (KRS or LysRS).
[0061] SEQ ID NO:12 is the amino acid sequence of a truncated human
KRS (residues 70-584 of full-length KRS).
[0062] SEQ ID NO:13 is the amino acid sequence of truncated human
KRS having an insertion of the 180 amino acid E. coli flavodoxin
(pdb:1ahn) protein at the G130 position of KRS (Flavo-KRS).
[0063] SEQ ID NO:14 is the polynucleotide sequence that encodes the
Flavo-KRS monomer of SEQ ID NO:13.
BRIEF DESCRIPTION OF THE DRAWINGS
[0064] FIG. 1 is a schematic diagram which illustrates a mechanism
of mini-YRS-mediated cytokine signaling. In this model, the
dissociated monomer form of the homodimeric mini-YRS is the active
cytokine and the dimer is a nonfunctional receptor binding form.
Dimeric YRS with individual monomers are shown in light grey and
dark grey and the ELR motif for the light grey monomer is shown in
slightly darker grey.
[0065] FIGS. 2A-2C show the rational design of an exemplary
non-associating monomeric form of mini-YRS, and a disulfide link
non-dissociating dimeric form of mini-YRS. FIG. 2A shows the
structure of a mini-YRS dimer with individual monomers shown in
light grey and dark grey (PDB 1q11). FIG. 2B shows the structure of
the dimer interface with the three residue deletion (P159, L160,
L161; indicated by arrows)--these deletions generated an exemplary
non-associating monomer of YRS (.DELTA.159-161). FIG. 2C shows the
dimer interface, in which the Thr 130 was replaced with Cys, and
upon I.sub.2 oxidation formed a disulfide bond linkage across the
dimer interface to generate a non-dissociating dimer
(C130.sup.OX).
[0066] FIGS. 3A-3E shows the characterization of the .DELTA.159-161
and C130.sup.OX variants. FIG. 3A is a non-reducing SDS-PAGE
analysis showing .DELTA.159-161 and C130.sup.OX variants
electrophoresis as monomer and dimer, respectively. FIG. 3B is a
far-UV CD spectra of WT ( ), .DELTA.159-161 (.tangle-solidup.) and
C130.sup.OX (.box-solid.). FIG. 3C is a thermal melting CD spectra
of WT ( ) versus .DELTA.159-161 (.tangle-solidup.). FIG. 3D is a
near-UV CD spectra of WT ( ) versus .DELTA.159-161
(.tangle-solidup.). FIG. 3E is an amino acid activation assay
comparing activity of WT, .DELTA.159-161 and C130.sup.OX
variants.
[0067] FIGS. 4A-4C show the determination of dimer-monomer
equilibrium dissociation constants for WT min-YRS and
.DELTA.159-161 mini-YRS. FIG. 4A shows an analytical gel
chromatography of WT, .DELTA.159-161 and C130.sup.OX, in which the
WT and C130.sup.OX peaks correspond to dimeric mini-YRS and
.DELTA.159-161 peak corresponds to monomeric mini-YRS. Also shown
is the estimation of dimer-monomer equilibrium dissociation
constant for .DELTA.159-161 (4B) by gel filtration chromatography
and WT (4C) by gel chromatography in combination with
immunoblotting.
[0068] FIGS. 5A-5C illustrate the effects of WT, .DELTA.159-161 and
C130.sup.OX on PMN cell migration activity. In FIG. 5A, WT exhibits
bell-shaped concentration response consistent with previous
studies. In FIG. 5B, the monomeric .DELTA.159-161 YRS is
functionally active and shows no decrease in migration activity at
high concentrations. In FIG. 5C, the dimeric C130.sup.OX is unable
to stimulate cell migration.
[0069] FIG. 6 shows that C130.sup.OX inhibits WT mini-YRS-induced
PMN cell migration.
[0070] FIG. 7 shows that the monomeric .DELTA.159-161 YRS binds to
CXCR-1 and CXCR-2.
[0071] FIG. 8 shows that the dimeric C130.sup.OX YRS competes with
WT mini-YRS for binding to CXCR-1 and CXCR-2.
[0072] FIG. 9 illustrates the bases of the design of exemplary
T2-WRS variants that form stable monomers. The T2-WRS dimer is
shown in ribbon (grey), and certain relevant amino acids F260, Y201
and I278 located in the dimer interface are shown in stick figures
of these amino acids (center). The active site on each subunit,
which is also the proposed VE-cadherin binding site, is highlighted
by dashed ellipses on either side of the dimer interface. H130 is
located outside the active site, and when mutated to Arg, interacts
with E408 to induce a conformational change that is otherwise
induced by Zn2+ binding. The H130R mutation may therefore remove
the Zn.sup.2+ dependence of the T2-WRS and VE-cadherin interaction,
as shown by the data in FIG. 10C.
[0073] FIGS. 10A-10D show size exclusions chromatography that
illustrates the interaction of a monomer form of T2-WRS with the
VE-Cadherin EC1 domain. See Example 4. FIG. 10A shows the results
for T2-WRS. FIG. 10B shows the results for VE-Cadherin EC1 domain.
FIG. 10C shows the results for T2-WRS and VE-EC1 at 1:1 ratio with
0.1 mM Zn.sup.2+. FIG. 10D shows the results for T2-WRS and VE-EC1
at 1:1 ratio with 0.1 mM Zn.sup.2+ and 30 uM Trp-SA.
[0074] FIGS. 11A-11C show size exclusion chromatography analysis
confirming that T2-WRS variants F260EY201EI278E and F260EY201EH130R
exist as monomers in solution. WT T2-WRS (FIG. 11A),
F260EY201EI278E T2-WRS (FIG. 11B) and F260EY201EH130R T2-WRS (FIG.
11C) were loaded on Superdex200 HR 10/30 column and eluted at 0.5
mL min with a buffer containing 25 mM Tris-HCl (pH 8.0), 150 mM
NaCl. See Example 5.
[0075] FIG. 12 shows the results of an immunoprecipitation assay in
which monomers F260EY201EI278E T2-WRS and F260EY201EH130R T2-WRS
bind stronger to VE-EC1 than does the WT T2-WRS, in the absence of
Zinc. See Example 6.
[0076] FIG. 13 shows a tuber formation assay in which the
engineered T2-WRS monomers are active in reducing angiogenesis. WT
T2-WRS and its variants F260EY201EI278E and F260EY201EH130R were
tested at different concentration in 3B11 cells which were cultured
for 6.5 hours. See Example 7.
[0077] FIGS. 14A-14B show the results of experiments to determine
the dimer-monomer dissociation constant of T2-WRS using
concentrations ranging from 100 nM to 10 .mu.M, as shown in FIG.
14A. In FIG. 14B, the percentage of dimers was calculated and
plotted as a function of the protein concentration to determine the
dimer-monomer dissociation constant (K.sub.d=0.437.+-.0.03
.mu.M).
[0078] FIGS. 15A-15B show the dissociation constant for WT T2-WRS
(15A) and the monomer T2-WRS (15B), as measured by surface plasmon
resonance analysis (Biacore).
[0079] FIGS. 16A-16C show that WT T2-WRS and monomer T2-WRS induce
degradation of .beta.-catenin. FIG. 16A illustrates how dissociated
.beta.-catenin is degraded by the proteosome, and FIG. 16B shows
that treatment of VE-Cadherin expressing C8161 melanoma cells with
1 .mu.M of either WT T2-WRS or monomer T2-WRS (F260EY201EI278E)
caused a sharp decrease in .beta.-catenin protein levels. FIG. 16C
shows that even at 270 .mu.M (well above the 1 .mu.M concentration
used in this experiment), F260EY201EI278E T2-TrpRS is still
predominately in monomeric conformation. The estimated
dimer-monomer dissociation constant (Kd) for F260EY201EI278E
T2-TrpRS is greater than 1 mM.
[0080] FIG. 17 shows the results of a tuber formation assay using
various concentrations of WT-T2WRS. This assay demonstrates that
the most potent angiostatic activity of WT T2-TrpRS is at 50 nM, a
concentration at which WT T2-TrpRS has a predominately monomer
conformation according to its dimer-monomer dissociation constant
of 472 nM.
[0081] FIGS. 18A-18E show the results of an ab initio model of the
docking of the Gag-CA-CTD domain onto human KRS. The Gag binding
site is at the dimerization interface of KRS, suggesting that the
monomeric KRS is the functional unit for HIV Gag protein binding.
FIG. 18A shows a schematic of human KRS and the rigid-body docking
results of CTD on the human KRS structure by HEX, ZDOCK and Dot.
Each dot represents the core of docked CTD structures. FIG. 18B
shows the docking of CTD on human KRS in the refined space by
AutoDock. The energy distribution of each cluster of solutions is
shown below the image. FIG. 18C shows the molecular dynamics
refinement of the lowest energy model from AutoDock. After the MD
refinement, CTD moved 3 .ANG. towards the aminoacylation domain of
KRS and formed a tighter contact. The AutoDock solution of CTD and
of the anticodon-binding domain of human KRS are shown. The MD
final solution of CTD, and of anticodon-binding domain are also
shown; the region 220-260 in the catalytic domain of human KRS
includes a hydrophobic patch (231-245) that overlaps with the
characteristic motif-1 (238-260) in Class II AARSs. FIG. 18D shows
a surface representation of the final docking model. FIG. 18E shows
a closeup view of KRS/CTD complex model. Helices 1-4 of CTD were
colored from N-terminus (H1) to C-terminus (H4).
[0082] FIG. 19 shows a model of the human KRS/tRNA.sup.Lys3/Gag-CA
ternary complex. The NTD of Gag capsid (Gag-CA) is shown at top.
The N-terminal helix of human KRS is shown as a surface
representation. All Lys/Arg residues on the N-terminal helix
extension are shown in dark grey shading, with most of them facing
the bound tRNA. The arrows indicate the potential location of
N-terminal and C-terminal regions of Gag outside of the CA
structure.
[0083] FIGS. 20A-20D illustrate the engineering of human KRS into a
monomer. In FIG. 20A, the human KRS dimer is shown with one subunit
as a schematic cartoon and the other as a surface representation.
FIG. 20B shows the design of the mutagenesis on the peripheral
region of the dimer interface. The predicted CTD binding site is
located at the core of the KRS dimer interface (colored in grey).
The peripheral region of the dimer interface is shown in white,
with the selected sites of mutations in black. The corresponding
positions of these sites are also shown in the sequence scheme of
KRS. FIG. 20C shows flavodoxin insertion into human KRS. E. coli
Flavodoxin was inserted at the position of G310 on the peripheral
region of the KRS dimer interface. The linker was kept short to
reduce the potential structural flexibility. A model of the fused
Flavo-KRS is shown with the flavodoxin structure in dark grey
(right side, below the G310 residue). FIG. 20D shows an overlay of
Superdex 200 gel filtration profiles of human KRS mutants. Mutated
residues are underlined. All proteins were loaded at a
concentration range of 0.5-2 .mu.M. The vertical line gives the
position of the KRS dimer; only Flavo-KRS ran as a monomer. BSA is
bovine serum albumin.
[0084] FIGS. 21A-21B show the characterization of monomeric
Flavo-KRS. In FIG. 21A, E. coli flavodoxin and the purified
Flavo-KRS show a similar result (bright yellow color), indicating a
properly folded flavodoxin domain in the fusion protein. FIG. 21B
shows a crosslinking assay of Thr385Cys mutants of both native KRS
and Flavo-KRS; this assay was performed in the presence and absence
of the DTT reducing agent, and shows that Flavo-KRS does not form a
dimer in solution.
[0085] FIGS. 22A-22D show that monomeric Flavo-KRS retains Gag and
tRNA.sup.Lys3 binding. FIG. 22A illustrates a StrepII-tag pull-down
assay of binding to Gag.DELTA.P6 that has been immobilized on
Tactin beads through a D-desthiobiotin-eluatable tag. FIGS. 22B-D
show EMSA assays of full-length KRS (22B) and Flavo-KRS (22C)
binding to in vitro transcribed human tRNA.sup.Lys3. The binding
affinity shown in FIG. 22D was calculated from the percentage of
free/unbound tRNA on the gel.
DETAILED DESCRIPTION OF THE INVENTION
[0086] The practice of the present invention will employ, unless
indicated specifically to the contrary, conventional methods of
molecular biology and recombinant DNA techniques within the skill
of the art, many of which are described below for the purpose of
illustration. Such techniques are explained fully in the
literature. See, e.g., Sambrook, et al., Molecular Cloning: A
Laboratory Manual (2nd Edition, 1989); Maniatis et al., Molecular
Cloning: A Laboratory Manual (1982); DNA Cloning: A Practical
Approach, vol. I & II (D. Glover, ed.); Oligonucleotide
Synthesis (N. Gait, ed., 1984); Nucleic Acid Hybridization (B.
Hames & S. Higgins, eds., 1985); Transcription and Translation
(B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R.
Freshney, ed., 1986); A Practical Guide to Molecular Cloning (B.
Perbal, ed., 1984).
[0087] All publications, patents and patent applications cited
herein are hereby incorporated by reference in their entirety.
DEFINITIONS
[0088] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by those
of ordinary skill in the art to which the invention belongs.
Although any methods and materials similar or equivalent to those
described herein can be used in the practice or testing of the
present invention, preferred methods and materials are described.
For the purposes of the present invention, the following terms are
defined below.
[0089] The articles "a" and "an" are used herein to refer to one or
to more than one (i.e., to at least one) of the grammatical object
of the article. By way of example, "an element" means one element
or more than one element.
[0090] By "about" is meant a quantity, level, value, number,
frequency, percentage, dimension, size, amount, weight or length
that varies by as much as 30, 25, 20, 25, 10, 9, 8, 7, 6, 5, 4, 3,
2 or 1% to a reference quantity, level, value, number, frequency,
percentage, dimension, size, amount, weight or length.
[0091] An AARS polypeptide may be characterized as "substantially
monomeric" or "non-associating" if, for example, its ability to
dimerize with itself (i.e., homodimerize) or dimerize with a second
AARS polypeptide (e.g., heterodimerize with a full-length wild-type
YRS polypeptide of SEQ ID NO:1 or mini-YRS of SEQ ID NO:3) is
reduced by a statistically significant amount as compared to the
ability of a control AARS polypeptide to dimerize. In certain
embodiments, the control peptide may include a full-length
wild-type AARS polypeptide, or a naturally-occurring splice variant
or fragment that has the ability to dimerize. Hence, in certain
embodiments, a substantially monomeric AARS polypeptide may be
characterized by its reduced ability to dimerize with itself, as
compared to the ability of a full-length or truncated AARS
polypeptide to dimerize with itself, or a naturally-occurring
fragment to dimerize with itself, typically measured and compared
at a selected concentration of polypeptide (e.g., mini-YRS exists
predominantly as a dimer in solution at .mu.M concentrations). A
statistically significant reduction may include, for instance, a
10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%,
35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or
100% reduction or decrease in its ability to dimerize, including
all integers in between.
[0092] In certain embodiments, the AARS polypeptide is
substantially in a monomeric form, or substantially monomeric,
under physiological conditions or in solution. Examples of
physiological conditions include, without limitation, the in vivo
conditions encountered in blood or other tissues, the in vitro
conditions encountered in mammalian cell cultures, and other in
vitro conditions such as in a salt solution (e.g., 25 mM Tris-Cl
pH8.0, 150 mM NaCl) or a pharmaceutical formulation described
herein.
[0093] The term "biologically active fragment," as applied to
fragments of a reference polynucleotide or polypeptide sequence,
refers to a substantially monomeric AARS fragment that has at least
about 0.1, 0.5, 1, 2, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28,
30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98,
99, 100, 110, 120, 150, 200, 300, 400, 500, 600, 700, 800, 900,
1000% or more of the non-canonical activity of a reference
sequence. Included within the scope of the present invention are
monomeric and biologically active fragments of at least about 10,
11, 12, 13, 14, 15, 16, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200,
220, 240, 260, 280, 300, 320, 340, 360, 380, 400, 420, 440, 450,
460, 465 or more contiguous nucleotides or amino acid residues in
length of SEQ ID NOS:1, 3-5, 7-9, or 11-13 (or Table A), including
all integers in between, all or any portion of which encodes or
comprises a monomeric AARS polypeptide having a non-canonical
biological activity of a reference polynucleotide or polypeptide,
such as the monomeric reference polypeptides of SEQ ID NOS:4, 8-9,
or 13.
[0094] Hence, in certain embodiments, a biologically active and
substantially monomeric AARS polypeptide fragment of about 10, 11,
12, 13, 14, 15, 16, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 220,
240, 260, 280, 300, 320, 340, 360, 380, 400, 420, 440, 450, 460,
465 or more amino acid residues in length could contain only about
10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% AARS-specific
residues, such as about 10, 11, 12, 13, 14, 15, 16, 16, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70,
75, 80, 85, 90, 95, 100, 120, 140, 160, 180, 200, 220, 240, 260,
280, 300, 320, 340, 360, 380, 400, 420, 440, 460, or 470
AARS-specific residues, contiguous or non-contiguous, with the rest
of the fragment being made of any selected polypeptide
sequences.
[0095] Representative biologically active fragments generally
participate in an interaction, e.g., an intramolecular or an
inter-molecular interaction. An inter-molecular interaction can be
a specific binding interaction or an enzymatic interaction. An
inter-molecular interaction can be between an AARS polypeptide and
target molecule, such as a target molecule involved in modulation
of cell proliferation, modulation of apoptosis, modulation of cell
signaling, modulation of angiogenesis, modulation of cell
migration, modulation of cell binding, modulation of cellular
metabolism, modulation of cytokine production or activity, cytokine
receptor activity, and the like. Examples of target molecules
include CXCR-1 and CXCR-2 and VE-cadherin, among others. In certain
embodiments, a specific binding interaction as with the
extracellular domain EC1 of VE-cadherin.
[0096] In certain embodiments, a monomeric WRS or its biologically
active fragment may be characterized by its ability to bind to
VE-cadherin in the absence of Zn.sup.2+, in the presence of low
levels of zinc, or in the presence of a zinc chelator, i.e., the
interaction between the monomeric WRS polypeptide is characterized
by its relative Zn.sup.2+ independence, as compared to a dimer WRS
control, such as T2-WRS. Monomeric and biologically active
fragments of a WRS polypeptide include polypeptide fragments
comprising amino acid sequences with sufficient similarity or
identity to, or which are derived from, the amino acid sequences of
SEQ ID NOS:5 or 7-9, or are encoded by all or part of the
nucleotide sequence of SEQ ID NO:6, and which in certain
embodiments do not substantially dimerize with another WRS
polypeptide.
[0097] By "coding sequence" is meant any nucleic acid sequence that
contributes to the code for the polypeptide product of a gene. By
contrast, the term "non-coding sequence" refers to any nucleic acid
sequence that does not contribute to the code for the polypeptide
product of a gene.
[0098] Throughout this specification, unless the context requires
otherwise, the words "comprise," "comprises," and "comprising" will
be understood to imply the inclusion of a stated step or element or
group of steps or elements but not the exclusion of any other step
or element or group of steps or elements.
[0099] By "consisting of" is meant including, and limited to,
whatever follows the phrase "consisting of." Thus, the phrase
"consisting of" indicates that the listed elements are required or
mandatory, and that no other elements may be present. By
"consisting essentially of" is meant including any elements listed
after the phrase, and limited to other elements that do not
interfere with or contribute to the activity or action specified in
the disclosure for the listed elements. Thus, the phrase
"consisting essentially of" indicates that the listed elements are
required or mandatory, but that other elements are optional and may
or may not be present depending upon whether or not they materially
affect the activity or action of the listed elements.
[0100] The terms "complementary" and "complementarity" refer to
polynucleotides (i.e., a sequence of nucleotides) related by the
base-pairing rules. For example, the sequence "A-G-T," is
complementary to the sequence "T-C-A." Complementarity may be
"partial," in which only some of the nucleic acids' bases are
matched according to the base pairing rules. Or, there may be
"complete" or "total" complementarity between the nucleic acids.
The degree of complementarity between nucleic acid strands has
significant effects on the efficiency and strength of hybridization
between nucleic acid strands.
[0101] By "corresponds to" or "corresponding to" is meant (a) a
polynucleotide having a nucleotide sequence that is substantially
identical or complementary to all or a portion of a reference
polynucleotide sequence or encoding an amino acid sequence
identical to an amino acid sequence in a peptide or protein; or (b)
a peptide or polypeptide having an amino acid sequence that is
substantially identical to a sequence of amino acids in a reference
peptide or protein.
[0102] By "derivative" is meant a polypeptide that has been derived
from the basic sequence by modification, for example by conjugation
or complexing with other chemical moieties (e.g., pegylation) or by
post-translational modification techniques as would be understood
in the art. The term "derivative" also includes within its scope
alterations that have been made to a parent sequence including
additions or deletions that provide for functionally equivalent
molecules.
[0103] As used herein, the terms "function" and "functional" and
the like refer to a biological, enzymatic, or therapeutic
function.
[0104] By "gene" is meant a unit of inheritance that occupies a
specific locus on a chromosome and consists of transcriptional
and/or translational regulatory sequences and/or a coding region
and/or non-translated sequences (i.e., introns, 5' and 3'
untranslated sequences).
[0105] "Homology" refers to the percentage number of amino acids
that are identical or constitute conservative substitutions.
Homology may be determined using sequence comparison programs such
as GAP (Deveraux et al., 1984, Nucleic Acids Research 12, 387-395),
which is incorporated herein by reference. In this way sequences of
a similar or substantially different length to those cited herein
could be compared by insertion of gaps into the alignment, such
gaps being determined, for example, by the comparison algorithm
used by GAP.
[0106] The term "host cell" includes an individual cell or cell
culture that can be or has been a recipient of any recombinant
vector(s) or isolated polynucleotide of the invention. Host cells
include progeny of a single host cell, and the progeny may not
necessarily be completely identical (in morphology or in total DNA
complement) to the original parent cell due to natural, accidental,
or deliberate mutation and/or change. A host cell includes cells
transfected or infected in vivo or in vitro with a recombinant
vector or a polynucleotide of the invention. A host cell which
comprises a recombinant vector of the invention is a recombinant
host cell.
[0107] By "isolated" is meant material that is substantially or
essentially free from components that normally accompany it in its
native state. For example, an "isolated polynucleotide," as used
herein, includes a polynucleotide that has been purified from the
sequences that flank it in its naturally-occurring state, e.g., a
DNA fragment which has been removed from the sequences that are
normally adjacent to the fragment. Alternatively, an "isolated
peptide" or an "isolated polypeptide" and the like, as used herein,
includes the in vitro isolation and/or purification of a peptide or
polypeptide molecule from its natural cellular environment, and
from association with other components of the cell; i.e., it is not
significantly associated with in vivo substances.
[0108] By "obtained from" is meant that a sample such as, for
example, a polynucleotide extract or polypeptide extract is
isolated from, or derived from, a particular source of the subject.
For example, the extract can be obtained from a tissue or a
biological fluid isolated directly from the subject. "Derived" or
"obtained from" can also refer to the source of a polypeptide or
polynucleotide sequence. For instance, an isolated AARS polypeptide
of the present invention may be "derived" from the sequence
information of an AARS proteolytic fragment or AARS splice variant,
whether naturally-occurring or artificially generated, and may thus
comprise, consist essentially of, or consist of that sequence.
[0109] The term "oligonucleotide" as used herein refers to a
polymer composed of a multiplicity of nucleotide residues
(deoxyribonucleotides or ribonucleotides, or related structural
variants or synthetic analogues thereof) linked via phosphodiester
bonds (or related structural variants or synthetic analogues
thereof). Thus, while the term "oligonucleotide" typically refers
to a nucleotide polymer in which the nucleotide residues and
linkages between them are naturally occurring, it will be
understood that the term also includes within its scope various
analogues including, but not restricted to, peptide nucleic acids
(PNAs), phosphoramidates, phosphorothioates, methyl phosphonates,
2-O-methyl ribonucleic acids, and the like. The exact size of the
molecule can vary depending on the particular application. An
oligonucleotide is typically rather short in length, generally from
about 10 to 30 nucleotide residues, but the term can refer to
molecules of any length, although the term "polynucleotide" or
"nucleic acid" is typically used for large oligonucleotides.
[0110] The term "operably linked" as used herein means placing a
structural gene under the regulatory control of a promoter, which
then controls the transcription and optionally translation of the
gene. In the construction of heterologous promoter/structural gene
combinations, it is generally preferred to position the genetic
sequence or promoter at a distance from the gene transcription
start site that is approximately the same as the distance between
that genetic sequence or promoter and the gene it controls in its
natural setting; i.e., the gene from which the genetic sequence or
promoter is derived. As is known in the art, some variation in this
distance can be accommodated without loss of function. Similarly,
the preferred positioning of a regulatory sequence element with
respect to a heterologous gene to be placed under its control is
defined by the positioning of the element in its natural setting;
i.e., the genes from which it is derived.
[0111] The recitation "polynucleotide" or "nucleic acid" as used
herein designates mRNA, RNA, cRNA, cDNA or DNA. The term typically
refers to polymeric form of nucleotides of at least 10 bases in
length, either ribonucleotides or deoxynucleotides or a modified
form of either type of nucleotide. The term includes single and
double stranded forms of DNA.
[0112] The terms "polynucleotide variant" and "variant" and the
like refer to polynucleotides displaying substantial sequence
identity with a reference polynucleotide sequence or
polynucleotides that hybridize with a reference sequence under
stringent conditions that are defined hereinafter. These terms also
encompass polynucleotides that are distinguished from a reference
polynucleotide by the addition, deletion or substitution of at
least one nucleotide. Accordingly, the terms "polynucleotide
variant" and "variant" include polynucleotides in which one or more
nucleotides have been added or deleted, or replaced with different
nucleotides. In this regard, it is well understood in the art that
certain alterations inclusive of mutations, additions, deletions
and substitutions can be made to a reference polynucleotide whereby
the altered polynucleotide retains the biological function or
activity of the reference polynucleotide. Polynucleotide variants
include, for example, polynucleotides having at least 50% (and at
least 51% to at least 99% and all integer percentages in between)
sequence identity with the sequence set forth in SEQ ID NO:2, 6, or
13, or portions thereof that encode a substantially monomeric and
biologically active fragment of an AARS polypeptide. The terms
"polynucleotide variant" and "variant" also include naturally
occurring allelic variants.
[0113] "Polypeptide," "polypeptide fragment," "peptide" and
"protein" are used interchangeably herein to refer to a polymer of
amino acid residues and to variants and synthetic analogues of the
same. Thus, these terms apply to amino acid polymers in which one
or more amino acid residues are synthetic non-naturally occurring
amino acids, such as a chemical analogue of a corresponding
naturally occurring amino acid, as well as to naturally-occurring
amino acid polymers.
[0114] The term "aminoacyl-tRNA synthetase" (AARS) refers generally
to enzymes that in their natural or wild-type form are capable of
catalyzing the esterification of a specific amino acid or its
precursor to one of all its compatible cognate tRNAs to form an
aminoacyl-tRNA. In this "canonical" activity, aminoacyl-tRNA
synthetases catalyse a two-step reaction: first, they activate
their respective amino acid by forming an aminoacyl-adenylate, in
which the carboxyl of the amino acid is linked in to the
alpha-phosphate of ATP by displacing pyrophosphate, and then, when
the correct tRNA is bound, the aminoacyl group of the
aminoacyl-adenylate is transferred to the 2' or 3' terminal OH of
the tRNA.
[0115] Class I aminoacyl-tRNA synthetases typically have two highly
conserved sequence motifs. These enzymes aminoacylate at the 2'-OH
of an adenosine nucleotide, and are usually monomeric or dimeric.
Class II aminoacyl-tRNA synthetases typically have three highly
conserved sequence motifs. These enzymes aminoacylate at the 3'-OH
of the same adenosine, and are usually dimeric or tetrameric. The
active sites of class II enzymes are mainly made up of a
seven-stranded anti-parallel .beta.-sheet flanked by
.alpha.-helices. Although phenylalanine-tRNA synthetase is class
II, it aminoacylates at the 2'-OH.
[0116] Monomeric AARS polypeptides of the present invention include
tyrosyl-tRNA synthetase (YRS), a tryptophanyl-tRNA synthetase
(WRS), a glutaminyl-tRNA synthetase (QRS), a glycyl-tRNA synthetase
(GlyRS), a histidyl-tRNA synthetase (HisRS), a seryl-tRNA
synthetase (SRS), a phenylalanyl-tRNA synthetase (PheRS), an
alanyl-tRNA synthetase (AlaRS), an asparaginyl-tRNA synthetase
(AsnRS), an aspartyl-tRNA synthetase (AspRS), a cysteinyl-tRNA
synthetase (CysRS), a glutamyl-tRNA synthetase (ERS), a prolyl-tRNA
synthetase (ProRS), an arginyl-tRNA synthetase (RRS), an
isoleucyl-tRNA synthetase (IRS), a leucyl-tRNA synthetase (LRS), a
lysyl-tRNA synthetase (KRS), a threonyl-tRNA synthetase (TRS), a
methionyl-tRNA synthetases (MRS), or a valyl-tRNA synthetase (VRS).
The wild-type sequences of these AARS polypeptides are known in the
art.
[0117] The recitations "polypeptides" "polypeptide fragments,"
"truncated polypeptides" or "variants thereof" encompass, without
limitation, substantially monomeric or non-associating AARS
polypeptides having an amino acid sequence that shares at least 50%
(and at least 51% to at least 99% and all integer percentages in
between) sequence identity with a reference sequences set forth in
SEQ ID NOS:1, 3-5, 7-9, or 11-13 (or Table A), such as fragments
having at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120,
140, 160, 180, 200, 220, 240, 260, 280, 300, 350, 400 or more
contiguous amino acids of the reference sequences, including all
integers in between. These recitations further encompass natural
allelic variation of AARS polypeptides that may exist and occur
from one genus or species to another.
[0118] Monomeric AARS polypeptides, including truncations and/or
variants thereof, encompass polypeptides that exhibit at least
about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 110%,
120%, 130%, 140%, 150%, 200%, 300%, 400%, 500%, 600%, 700%, 800%,
900%, 1000% or more of the specific biological activity (e.g., a
CXC receptor agonist activity) of a reference monomeric AARS
polypeptide, such as the exemplary monomeric polypeptide of SEQ ID
NOS:4, 8-9, and 13. In certain exemplary embodiments, AARS-related
biological activity may be quantified, for example, by measuring
the ability of a substantially monomeric AARS polypeptide (e.g.,
WRS) to bind to VE-cadherin, or to reduce angiogenesis (see, e.g.,
Example 4), among other activities apparent from the description
herein.
[0119] In still further exemplary embodiments, AARS-related
biological activity may be quantified, for example, by measuring
the ability of a substantially monomeric AARS polypeptide (e.g.,
YRS) to bind to CXCR-1 or CXCR-2, to agonize the activity of CXCR-1
or CXCR-2, or to increase polymorphonuclear cell migration (see,
e.g., Example 2), among other activities apparent from the
description herein. CXCR-1 or CXCR-2 mediated biological activities
include, for example, intracellular Ca.sup.2+ mobilization,
phosphoinositide hydrolysis, chemotaxis, exocytosis,
phosphorylation, desensitization, .beta.-arrestin translocation and
internalization, any one or more of which can be modulated by a
monomeric AARS polypeptide. Certain KRS monomers can be tested for
their ability to bind HIV-Gag and/or tRNA.sup.Lys3 and/or to
facilitate incorporation of tRNA.sup.Lys3 into the HIV virion.
[0120] Monomeric AARS polypeptides, including truncations and/or
variants thereof, having substantially reduced biological activity
relative to a reference AARS polypeptide are those that exhibit
less than about 25%, 10%, 5% or 1% of the specific activity of a
reference AARS polypeptide (i.e., having a non-canonical
activity).
[0121] The recitation polypeptide "variant" refers to polypeptides
that are distinguished from a reference polypeptide by the
addition, deletion or substitution of at least one amino acid
residue. In certain embodiments, a polypeptide variant is
distinguished from a reference polypeptide by one or more
substitutions, which may be conservative or non-conservative. In
certain embodiments, the polypeptide variant comprises conservative
substitutions and, in this regard, it is well understood in the art
that some amino acids may be changed to others with broadly similar
properties without changing the nature of the activity of the
polypeptide. Polypeptide variants also encompass polypeptides in
which one or more amino acids have been added or deleted, or
replaced with different amino acid residues.
[0122] The present invention contemplates the use of variants of
full-length AARS polypeptides, truncated fragments of full-length
AARS polypeptides, splice variants, fragments, and variants of such
fragments, as well as their related biologically active fragments,
which are substantially monomeric in form, i.e., they do not
substantially dimerize with another AARS polypeptide, typically
under physiological conditions or in solution. Monomeric and
biologically active fragments of an AARS polypeptide include
peptides comprising amino acid sequences sufficiently similar to,
or derived from, the amino acid sequences of a (putative)
full-length or wild-type AARS polypeptide sequence (see, e.g.,
Table A), or from exemplary monomeric AARS polypeptides (e.g., SEQ
ID NOS:4, 8-9, and 13).
[0123] Typically, biologically active fragments comprise a domain
or motif with at least one activity of an AARS polypeptide and may
include one or more (and in some cases all) of the various active
domains, and include fragments having the ability to interact with
or agonize CXC receptors such as CXCR-1 and/or CXCR-1, stimulate
PMNC migration, stimulate angiogenesis, interact with VE-cadherin,
reduce angiogenesis, or other activity described herein. In some
cases, monomeric and biologically active fragments of an AARS
polypeptide have a non-canonical biological activity that is unique
to the particular monomeric fragment or variant, such that the
full-length or dimeric forms of the AARS polypeptide may or may not
have that activity, or may have it to a lesser degree. In certain
cases, the biological activity may be revealed by separating the
biologically active AARS polypeptide fragment from the other
full-length AARS polypeptide sequences, or by altering certain
residues of the AARS wild-type polypeptide sequence to unmask the
biologically active domains, such as to prevent or reduce
dimerization between AARS polypeptides. In certain embodiments, a
monomeric and biologically active fragment comprises an angiogenic
response-modulating sequence, domain, or motif, such as a domain
that interacts with VE-cadherin, which may or not be possessed by a
dimeric polypeptide. In certain embodiments, a monomeric and
biologically active fragment comprises a cytokine-modulatory
sequence, domain, or motif, such as a domain that interacts with
and agonizes CXC receptors such as CXCR-1 and/or CXCR-1, which may
or may not be possessed by a dimeric polypeptide. Additional
examples of motifs include the Glu-Leu-Arg (ELR) motif. Suitably,
the monomeric and biologically-active fragment has no less than
about 1%, 10%, 25%, 50% of an activity of a reference AARS
polypeptide from which it is derived.
[0124] The recitations "sequence identity" or, for example,
comprising a "sequence 50% identical to," as used herein, refer to
the extent that sequences are identical on a
nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis
over a window of comparison. Thus, a "percentage of sequence
identity" may be calculated by comparing two optimally aligned
sequences over the window of comparison, determining the number of
positions at which the identical nucleic acid base (e.g., A, T, C,
G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser,
Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu,
Asn, Gln, Cys and Met) occurs in both sequences to yield the number
of matched positions, dividing the number of matched positions by
the total number of positions in the window of comparison (i.e.,
the window size), and multiplying the result by 100 to yield the
percentage of sequence identity.
[0125] Terms used to describe sequence relationships between two or
more polynucleotides or polypeptides include "reference sequence",
"comparison window", "sequence identity", "percentage of sequence
identity" and "substantial identity". A "reference sequence" is at
least 12 but frequently 15 to 18 and often at least 25 monomer
units, inclusive of nucleotides and amino acid residues, in length.
Because two polynucleotides may each comprise (1) a sequence (i.e.,
only a portion of the complete polynucleotide sequence) that is
similar between the two polynucleotides, and (2) a sequence that is
divergent between the two polynucleotides, sequence comparisons
between two (or more) polynucleotides are typically performed by
comparing sequences of the two polynucleotides over a "comparison
window" to identify and compare local regions of sequence
similarity. A "comparison window" refers to a conceptual segment of
at least 6 contiguous positions, usually about 50 to about 100,
more usually about 100 to about 150 in which a sequence is compared
to a reference sequence of the same number of contiguous positions
after the two sequences are optimally aligned. The comparison
window may comprise additions or deletions (i.e., gaps) of about
20% or less as compared to the reference sequence (which does not
comprise additions or deletions) for optimal alignment of the two
sequences. Optimal alignment of sequences for aligning a comparison
window may be conducted by computerized implementations of
algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin
Genetics Software Package Release 7.0, Genetics Computer Group, 575
Science Drive Madison, Wis., USA) or by inspection and the best
alignment (i.e., resulting in the highest percentage homology over
the comparison window) generated by any of the various methods
selected. Reference also may be made to the BLAST family of
programs as for example disclosed by Altschul et al., 1997, Nucl.
Acids Res. 25:3389. A detailed discussion of sequence analysis can
be found in Unit 19.3 of Ausubel et al., "Current Protocols in
Molecular Biology," John Wiley & Sons Inc, 1994-1998, Chapter
15.
[0126] A "subject," as used herein, includes any animal that
exhibits a symptom, or is at risk for exhibiting a symptom, which
can be treated with a substantially monomeric AARS polypeptide of
the invention. Suitable subjects (patients) include laboratory
animals (such as mouse, rat, rabbit, or guinea pig), farm animals,
and domestic animals or pets (such as a cat or dog). Non-human
primates and, preferably, human patients, are included.
[0127] An "effective concentration" of a substantially monomeric
AARS polypeptide refers to an amount that is capable of altering a
desired biological activity or response in any desired way, as
compared to a control polypeptide or no polypeptide, whether in a
cell in vitro or ex vivo, or in a cell in a subject. One
illustrative example of a biological activity includes agonizing
the activity of CXC receptors such as CXCR-1 and/or CXCR-2, similar
to the pro-inflammatory chemokine interleukin-8 (IL-8). Another
illustrative example of a biological activity includes inhibiting
or reducing angiogenesis. Other examples include, without
limitation, modulation of cell proliferation, modulation of
apoptosis, modulation of cell signaling, modulation of cell
migration, modulation of cell binding, modulation of cellular
metabolism, modulation of inflammation, and the like
[0128] An "immune cell" includes any cell of the vertebrate immune
system, including lymphocytes such as B-cells, killer T-cells
(i.e., CD8+ T-cells), helper T-cells (i.e., CD4+ T-cells, including
T.sub.h1 and T.sub.h2 cells), natural killer cells, and
.gamma..delta. T-cells, monocytes, macrophages, neutrophils,
dendritic cells, mast cells, eosinophils, and basophils.
[0129] A "megakaryocyte" refers generally to a bone marrow cell
that is responsible for the production of blood thrombocytes (i.e.,
platelets), which are necessary for normal blood clotting.
Megakaryocytes typically account for 1 out of 10,000 bone marrow
cells. Megakaryocytes are derived from pluripotent hematopoietic
stem cell precursor cells in the bone marrow. Thrombopoietin (TPO)
is the primary signal for megakaryocyte production, i.e., TPO is
sufficient but not absolutely necessary for inducing
differentiation of progenitor cells in the bone marrow towards a
final megakaryocyte phenotype. Other molecular signals for
megakaryocyte differentiation include GM-CSF, IL-3, IL-6, IL-11,
chemokines (SDF-1; FGF-4), and erythropoietin.
[0130] Megakaryocytes are believed to develop through the following
lineage: CFU-Me (pluripotential hematopoietic stem cell or
hemocytoblast)->megakaryoblast->promegakaryocyte->megakaryocyte.
At the megakaryoblast stage, the cell loses its ability to divide,
but is still able to replicate its DNA and continue development,
becoming polyploid. Upon maturation, megakaryocytes begin the
process of producing platelets, or thrombocytes. Thrombopoietin
plays a role in inducing the megakaryocyte to form small
proto-platelet processes, or cytoplasmic internal membranes for
storing platelets prior to release. Upon release, each of these
proto-platelet processes can give rise to 2000-5000 new platelets.
Overall, about 2/3 of the newly-released platelets will remain in
circulation and about 1/3 will be sequestered by the spleen. After
releasing the platelets, the remaining cell nucleus typically
crosses the bone marrow barrier to the blood and is consumed in the
lung by alveolar macrophages. Megakaryocytopenia, also referred to
as megakaryophthisis, is a scarcity of megakaryocytes in the bone
marrow.
[0131] An "erythrocyte" refers to a red blood cell that consists
mainly of hemoglobin, a complex metalloprotein containing heme
groups whose iron atoms temporarily link to oxygen molecules
(O.sub.2) in the lungs. Erythrocytes are produced by a process
called erythropoiesis, in which they develop from committed stem
cells through reticulocytes to mature erythrocytes in about 7 days
and live a total of about 100-120 days. "Polycythemias" (or
erythrocytoses) are diseases characterized by a surplus of
erythrocytes, in which the increased viscosity of the blood can
cause a number of symptoms. "Anemias" are diseases characterized by
low oxygen transport capacity of the blood, because of low red cell
count or some abnormality of the red blood cells or the
hemoglobin.
[0132] A "granulocyte" refers to a white blood cell that is
characterized by the presence of granules in its cytoplasm.
Granulocytes are also referred to as polymorphonuclear leukocytes
(PMN or PML), because of the varying shapes of the nuclei. Examples
of granulocytes include neutrophils, eosinophils, and
basophils.
[0133] A "neutrophil," or neutrophil granulocyte, refers generally
to an abundant type of white blood cells in humans, which, together
with basophils and eosinophils, form part of the polymorphonuclear
cell family (PMNs). Neutrophils can be readily identified according
to their unique staining characteristics on hematoxylin and eosin
(H&E) histological or cytological preparations. Neutrophils are
normally found in the blood stream, but are one of the first group
of inflammatory cells to migrate toward inflammation sites during
the beginning (i.e., acute) phase of inflammation, mainly as a
result of infection or cancer. Typically, neutrophils first migrate
through the blood vessels, and then through interstitial tissues,
following chemical signals (e.g., interleukin-8 (IL-8),
interferon-gamma (IFN-gamma), and C5a) that originate at the site
of inflammation. "Neutropenia" refers to the presence of low
neutrophil counts, which may result from a congenital (genetic)
disorder, or may develop due to other conditions, as in the case of
aplastic anemia or some kinds of leukemia. "Neutrophilia" refers to
an abnormally high neutrophil count.
[0134] "Eosinophils," also called eosinophilic leukocytes, refer to
leukocytes that have coarse round granules of uniform size within
their cytoplasm, and which typically have a bilobate (two-lobed)
nucleus. The cytoplasmic granules of eosinophils stain red with the
dye eosin. Eosinophils normally constitute about 1% to about 3% of
the peripheral blood leukocytes, at a count of about 350 to 650 per
cubic millimeter. Eosinophil counts in blood often rise above the
normal range during allergic reactions and parasitic infections,
such as worms. "Eosinopenia" refers to a form of agranulocytosis in
which the number of eosinophil granulocyte is lower than expected.
"Eosinophilia" refers to an abnormally high number of eosinophils
in the blood. For example, eosinophilia can be categorized as mild
(less than about 1500 eosinophils per cubic millimeter), moderate
(about 1500 to about 5000 per cubic millimeter), or severe (more
than about 5000 per cubic millimeter). In primary eosinophilia, the
increased production of eosinophils is typically due to an
abnormality in hematopoietic stem cells, such as in eosinophilic
leukemia. In secondary eosinophilia, the increased production of
eosinophils is typically due to a reactive process driven by
cytokines.
[0135] Basophils, also called basophilic leukocytes, refer to
leukocytes that have coarse bluish-black granules of uniform size
within the cytoplasm, and which typically have a bilobate
(two-lobed) nucleus. The cytoplasmic granules of basophils stain
with basic dyes. Basophils normally constitute about 0.5% to 3% of
the peripheral blood leukocytes. Basophils store and release
histamine and serotonin, among other chemicals. Basophils are
capable of ingesting foreign particles, and also produce, store and
release heparin, serotonin, and histamine. The release of
inflammatory chemicals such as heparin and histamine is often
associated with asthma and allergies. Basophils are produced
continually by stem cells in the bone marrow. "Basopenia" refers to
a low basophil count (e.g., less than about 0.01.times.10.sup.9 per
liter of blood), and "basophilia" refers to a high basophil count
(e.g., more than about 10.sup.10 per liter of blood).
[0136] "Lymphocytes" refer generally to white blood cells of the
vertebrate immune system, and include B-cells, T-cells (e.g.,
helper T-cells, cytotoxic T-cells, .gamma..delta. T-cells), and
natural killer (NK) cells. Generally, and merely for illustrative
purposes, B-cells produce and secrete antibodies, T-helper cells
release cytokines and growth factors that regulate other immune
cells, cytotoxic T-cells (CTLs) lyse virally infected cells, tumor
cells and allografts, and NK cells lyse virally infected cells and
tumor cells. "Lymphocytopenia" is characterized by abnormally low
level of lymphocytes in the blood. The normal total lymphocyte
count is typically about 1000 to 4800/.mu.L in adults, and about
3000 to 9500/.mu.L in children younger than 2 years. At age 6, the
lower limit of normal total lymphocyte count is about 1500/.mu.L.
Lymphocytopenia is often characterized by a total lymphocyte count
of <1000/.mu.L in adults or <3000/.mu.L in children younger
than 2 years. Specific examples of lymphocytopenia include
T-lymphocytopenia, in which there are too few T-cells (e.g., CD4+
T-cell counts below about 300 cells/.mu.L) but often normal numbers
of other lymphocytes, B lymphocytopenia, in which there are too few
B lymphocytes but often normal numbers of other lymphocytes, and NK
lymphocytopenia, in which there are there are too few natural
killer cells but often normal numbers of other lymphocytes.
[0137] "Lymphocytosis" refers to an abnormally high lymphocyte
count, often characterized by a total lymphocyte count that is more
than 40% above normal. In adults, absolute lymphocytosis is
typically present when the absolute lymphocyte count is greater
than 4000 per microliter, in older children greater than 7000 per
microliter, and in infants greater than 9000 per microliter.
Relative lymphocytosis may occur when there is a higher proportion
(greater than 40%) of lymphocytes among the white blood cells, and
when lymphocyte count (ALC) is normal (less than about 4000 per
microliter).
[0138] The term "modulating" includes "increasing" or
"stimulating," as well as "decreasing" or "reducing," typically in
a statistically significant or a physiologically significant
amount.
[0139] By "enhance" or "enhancing," or "increase" or "increasing,"
or "stimulate" or "stimulating," refers generally to the ability of
one or agents or compositions to produce or cause a greater
physiological response (i.e., downstream effects) in a cell, as
compared to the response caused by either no monomeric AARS
polypeptide or a control molecule/composition. Examples of
measurable physiological responses include increased levels or
activity of CXC receptors such as CXCR-1 and CXCR-2, increased
migration of PMNCs such as leukocytes, or increases in an
inflammatory or angiogenic response. Other examples will be
apparent from the understanding in the art and the description
herein. An "increased" or "enhanced" amount is typically a
"statistically significant" amount, and may include an increase
that is 1.1, 1.2, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 or more
times (e.g., 500, 1000 times) (including all integers and decimal
points in between and above 1), e.g., 1.5, 1.6, 1.7. 1.8, etc.) the
amount produced by no monomeric AARS polypeptide (the absence of an
agent) or a control composition.
[0140] The term "reduce" or "inhibit" may relate generally to the
ability of one or more monomeric AARS polypeptides of the invention
to "decrease" a relevant physiological or cellular response,
including a symptom of a disease or condition described herein, as
measured according to routine techniques in the diagnostic art.
Relevant physiological or cellular responses (in vivo or in vitro)
will be apparent to persons skilled in the art, and may include,
for example, reductions in inflammation or other physiological
response. Also included, for example, are reductions in
angiogenesis. Merely by way of illustration, exemplary symptoms may
include reductions in tumor growth, often associated with decreased
angiogenesis. A "decrease" in a response may be statistically
significant as compared to the response produced by no monomeric
AARS polypeptide or a control composition, and may include a 1%,
2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%,
17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,
70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease, including all
integers in between.
[0141] As noted above, also included are increases in migration,
such as the migration induced by chemokine receptor signaling. Also
included are reductions in migration, such as the migration induced
by angiogenic signaling. "Migration" refers to cellular migration,
a process that can be measured according to routine in vitro
assays, as described herein and known in the art. Migration also
refers to in vivo migration, such as the migration of cells from
one tissue to another tissue (e.g., from bone marrow to peripheral
blood, or from peripheral blood to a particular tissue), or from a
site within one tissue to another site within the same tissue.
Migration in vivo (e.g., chemotaxis) often occurs in a response to
infection or damaged/irritated tissue, or in response to angiogenic
signals.
[0142] "Treatment" or "treating," as used herein, includes any
desirable effect on the symptoms or pathology of a disease or
condition associated with the modulatory activities of a monomeric
AARS polypeptide as described herein, and may include even minimal
changes or improvements in one or more measurable markers of the
disease or condition being treated. "Treatment" or "treating" does
not necessarily indicate complete eradication or cure of the
disease or condition, or associated symptoms thereof. The subject
receiving this treatment is any animal in need, including primates,
in particular humans, and other mammals such as equines, cattle,
swine and sheep; and poultry and pets in general. Exemplary markers
of clinical improvement include an altered (e.g., increased or
decreased) inflammatory or immune response.
[0143] In certain embodiments, monomeric AARS polypeptides possess
angiostatic activity, and can be used to treat essentially any
condition that would benefit from decreased angiogenesis. For
example, angiostatic compositions of the invention may be used in
treating or ameliorating the symptoms of disease conditions which
rely upon angiogenesis and/or neovascularization, such as treating
a solid tumor or tumor metastasis. The angiostatic compositions may
also be used to treat conditions characterized by abnormal
angiogenesis, such as rheumatoid arthritis, other arthritides,
psoriasis, hyperangiogenic diseases, diabetic retinopathy,
retinopathy of prematurity, ischemic retinopathy, macular
degeneration, diabetic nephropathy. Further still, angiostatic
compositions of the invention may be used to oppose the angiogenic
activity of endogenous and/or exogenous angiogenic factors.
[0144] By "vector" is meant a polynucleotide molecule, preferably a
DNA molecule derived, for example, from a plasmid, bacteriophage,
yeast or virus, into which a polynucleotide can be inserted or
cloned. A vector preferably contains one or more unique restriction
sites and can be capable of autonomous replication in a defined
host cell including a target cell or tissue or a progenitor cell or
tissue thereof, or be integrable with the genome of the defined
host such that the cloned sequence is reproducible. Accordingly,
the vector can be an autonomously replicating vector, i.e., a
vector that exists as an extra-chromosomal entity, the replication
of which is independent of chromosomal replication, e.g., a linear
or closed circular plasmid, an extra-chromosomal element, a
mini-chromosome, or an artificial chromosome. The vector can
contain any means for assuring self-replication. Alternatively, the
vector can be one which, when introduced into the host cell, is
integrated into the genome and replicated together with the
chromosome(s) into which it has been integrated. A vector system
can comprise a single vector or plasmid, two or more vectors or
plasmids, which together contain the total DNA to be introduced
into the genome of the host cell, or a transposon. The choice of
the vector will typically depend on the compatibility of the vector
with the host cell into which the vector is to be introduced. In
the present case, the vector is preferably one which is operably
functional in a bacterial cell. The vector can also include a
selection marker such as an antibiotic resistance gene that can be
used for selection of suitable transformants.
[0145] The terms "wild-type" and "naturally occurring" are used
interchangeably to refer to a gene or gene product that has the
characteristics of that gene or gene product when isolated from a
naturally occurring source. A wild-type gene or gene product (e.g.,
a polypeptide) is that which is most frequently observed in a
population and is thus arbitrarily designed the "normal" or
"wild-type" form of the gene.
Aminoacyl-tRNA Synthetase Polypeptides
[0146] The present invention relates generally to isolated and
substantially monomeric aminoacyl-tRNA synthetases (AARS)
polypeptides having non-canonical biological activities,
polynucleotides encoding such polypeptides, binding agents that
bind such polypeptides, analogs, variants and fragments of such
polypeptides, etc., as well as compositions and methods of using
any of the foregoing. An AARS polypeptide is typically
characterized as monomeric when it does not substantially dimerize
with itself or with a second AARS polypeptide, as described
herein.
[0147] As noted above, monomeric AARS polypeptides of the present
invention include tyrosyl-tRNA synthetase (YRS), a
tryptophanyl-tRNA synthetase (WRS), a glutaminyl-tRNA synthetase
(QRS), a glycyl-tRNA synthetase (GlyRS), a histidyl-tRNA synthetase
(HisRS), a seryl-tRNA synthetase (SRS), a phenylalanyl-tRNA
synthetase (PheRS), an alanyl-tRNA synthetase (AlaRS), an
asparaginyl-tRNA synthetase (AsnRS), an aspartyl-tRNA synthetase
(AspRS), a cysteinyl-tRNA synthetase (CysRS), a glutamyl-tRNA
synthetase (ERS), a prolyl-tRNA synthetase (ProRS), an arginyl-tRNA
synthetase (RRS), an isoleucyl-tRNA synthetase (IRS), a leucyl-tRNA
synthetase (LRS), a lysyl-tRNA synthetase (KRS), a threonyl-tRNA
synthetase (TRS), a methionyl-tRNA synthetases (MRS), or a
valyl-tRNA synthetase (VRS). Exemplary wild-type sequences of these
AARS polypeptides are known in the art, and are referred to in
Table A below.
TABLE-US-00001 TABLE A Human AARS Polypeptide Sequences AARS
UniProtKB/Swiss-Prot AARS UniProtKB/Swiss-Prot YRS P54577
(SYYC_HUMAN) ProRS P07814 (SYEP_HUMAN) Q9Y2Z4 (SYYM_HUMAN) Q7L3T8
(SYPM_HUMAN) WRS P23381 (SYWC_HUMAN) RRS P54136 (SYRC_HUMAN) QRS
P47897 (SYQ_HUMAN) Q5T160 (SYRM_HUMAN) GlyRS P41250 (SYG_HUMAN) IRS
P41252 (SYIC_HUMAN) HisRS P12081 (SYHC_HUMAN) Q9NSE4 (SYIM_HUMAN)
SRS P49591 (SYSC_HUMAN) LRS Q9P2J5 (SYLC_HUMAN) Q9NP81 (SYSM_HUMAN)
Q15031 (SYLM_HUMAN) PheRS O95363 (SYFM_HUMAN) KRS Q15046
(SYK_HUMAN) Q9Y285 (SYFA_HUMAN) TRS P26639 (SYTC_HUMAN) Q9NSD9
(SYFB_HUMAN) Q9BW92 (SYTM_HUMAN) AlaRS P49588 (SYAC_HUMAN) A2RTX5
(SYTC2_HUMAN) Q5JTZ9 (SYAM_HUMAN) MRS P56192 (SYMC_HUMAN) AsnRS
O43776 (SYNC_HUMAN) VRS P26640 (SYVC_HUMAN) Q96I59 (SYNM_HUMAN)
Q5ST30 (SYVM_HUMAN) AspRS P14868 (SYDC_HUMAN) Q6PI48 (SYDM_HUMAN)
CysRS P49589 (SYCC_HUMAN) Q9HA77 (SYCM_HUMAN) ERS P07814
(SYEP_HUMAN) Q5JPH6 (SYEM_HUMAN)
[0148] As one exemplary AARS polypeptide, tyrosyl-tRNA synthetases
(YRS or TyrRS) belong to the class I tRNA synthetase family, which
has two highly conserved sequence motifs at the active site, HIGH
and KMSKS. Class I tRNA synthetases aminoacylate at the 2'-OH of an
adenosine nucleotide, and are usually monomeric or dimeric (one or
two subunits, respectively).
[0149] The human tyrosyl-tRNA synthetase is composed of three
domains: 1) an amino-terminal Rossmann fold domain that is
responsible for formation of the activated E.Tyr-AMP intermediate
and is conserved among bacteria, archeae, and eukaryotes; 2) a tRNA
anticodon recognition domain that has not been conserved between
bacteria and eukaryotes; and 3) a carboxyl-terminal domain that is
unique to the human tyrosyl-tRNA synthetase, and whose primary
structure is 49% identical to the putative human cytokine
endothelial monocyte-activating protein II, 50% identical to the
carboxyl-terminal domain of methionyl-tRNA synthetase from
Caenorhabditis elegans, and 43% identical to the carboxyl-terminal
domain of Arc1p from Saccharomyces cerevisiae.
[0150] The first two domains of the human tyrosyl-tRNA synthetase
are 52, 36, and 16% identical to tyrosyl-tRNA synthetases from S.
cerevisiae, Methanococcus jannaschii, and Bacillus
stearothermophilus, respectively. Nine of fifteen amino acids known
to be involved in the formation of the tyrosyl-adenylate complex in
B. stearothermophilus are conserved across all of the organisms,
whereas amino acids involved in the recognition of tRNA.sup.Tyr are
not conserved. Kinetic analyses of recombinant human and B.
stearothermophilus tyrosyl-tRNA synthetases expressed in
Escherichia coli indicate that human tyrosyl-tRNA synthetase
aminoacylates human but not B. stearothermophilus tRNA.sup.Tyr, and
vice versa. It is believed that the carboxyl-terminal domain of
human tyrosyl-tRNA synthetase evolved from gene duplication of the
carboxyl-terminal domain of methionyl-tRNA synthetase and may
direct tRNA to the active site of the enzyme.
[0151] Biological fragments of eukaryotic tyrosyl-tRNA synthetases
connect protein synthesis to cell-signaling pathways. These
fragments may be produced naturally by either alternative splicing
or proteolysis, or by artificial proteolytic treatment. For
example, the N-terminal fragment mini-YRS is capable of modulating
inflammatory responses in vivo. In addition, certain mutations in
the full-length YRS polypeptide sequence confer increased
inflammatory response-modulating activity on the reference sequence
(e.g., Y341A). Examples of truncated splice variants of the
full-length YRS polypeptide sequence include the SP1-SP5
polypeptides.
[0152] The full-length amino acid sequence of human tyrosyl-tRNA
synthetase is set forth in SEQ ID NO:1. The structure of human
mini-YRS (SEQ ID NO:3), which contains both the catalytic and the
anticodon recognition domain, has been reported to a resolution of
1.18 .ANG.. Whereas the catalytic domains of the human and
bacterial enzymes superimpose, the spatial disposition of the
anticodon recognition domain relative to the catalytic domain is
unique in mini-YRS relative to the bacterial orthologs. Certain
embodiments may exclude the YRS polypeptides of SEQ ID NO:1 or 3,
and/or certain YRS C-domain fragments.
[0153] Particular examples of biologically active YRS fragments
include, but are not limited to, C-terminally truncated
tyrosyl-tRNA synthetase polypeptides comprising or consisting of
amino acids 1-343, amino acids 1-344, amino acids 1-350, amino
acids 1-353, or amino acids 1-364 of the amino acid sequence set
forth in SEQ ID NO:1, in addition to the polypeptides of SEQ ID
NOS:3 and 4, which have been modified to be substantially monomeric
in form. Specific examples of YRS polypeptide variants include
full-length YRS polypeptides, or truncations or splice variants
thereof, having one or more amino acid substitutions selected from
an R93Q substitution, an I14L substitution, an N17G substitution,
an L271 substitution, an A85S substitution, and a V156L
substitution, in addition to combinations thereof, any of which can
be modified in a substantially monomeric form of a YRS
polypeptide.
[0154] As another exemplary AARS polypeptide, tryptophanyl-tRNA
synthetases (WRS or TrpRS), also referred to as tryptophan-tRNA
ligases, belong to the class I tRNA synthetase family.
Tryptophanyl-tRNA synthetase catalyzes the aminoacylation of
tRNA.sup.trp with tryptophan, an essential function in protein
synthesis. Human WRS has a kinase domain in the N-terminal region
and a serine phosphorylation site near the C-terminus.
[0155] Two main forms of human tryptophanyl-tRNA synthetase are
produced in vivo through alternative mRNA splicing, to yield the
full-length protein (SEQ ID NO: 5), and a fragment thereof, often
designated mini-WRS. Also included are human T1-WRS and T2-WRS (SEQ
ID NO:7), alternate splice variants that are produced from an
IFN-gamma-sensitive promoter, the latter being an N-terminally
truncated fragment of WRS, as well as monomeric variants of T2-WRS
(see, e.g., SEQ ID NOS:8 and 9). Other splice variants of human WRS
are known in the art (see, e.g., Liu et al., Nucleic Acids
Research, 32(2):719-27, 2004, herein incorporated by reference).
Certain embodiments exclude these naturally-occurring variants of
WRS, such as T2-WRS.
[0156] Structurally, full-length bacterial WRS contains three
parts, a canonical dinucleotide-binding fold, a dimer interface,
and a helical domain. This enzyme has enough structural homology to
tyrosyl-tRNA synthetase (YRS) that the two enzymes can be described
as conformational isomers. Structural elements interacting with the
activated amino acid, tryptophanyl-5' AMP, are almost exactly as
seen in the tyrosyl-5' AMP complex. Also, side chains that
recognize indole are also highly conserved, and require
reorientation of a "specificity-determining" helix containing a
conserved aspartate to assure selection of tryptophan versus
tyrosine. The carboxy terminus, which is disordered and therefore
not seen in YRS, forms part of the dimer interface in WRS (see
Doublie et al., Structure. 3:17-31, 1995).
[0157] The crystal structure of human T2-WRS has been reported at
2.5 .ANG. resolution. This variant shares a very low sequence
homology of 22% with Bacillus stearothermophilus WRS (bWRS),
however their overall structures are strikingly similar. Structural
comparison of T2-WRS with bWRS reveals substantial structural
differences in the substrate-binding pocket and at the entrance to
the pocket that play important roles in substrate binding and tRNA
binding. T2-WRS has a wide opening to the active site and adopts a
compact conformation similar to the closed conformation of bWRS.
Modeling studies indicate that tRNA binds with the dimeric enzyme
and interacts primarily with the connective polypeptide 1 of human
WRS via its acceptor arm and the .alpha.-helical domain of WRS via
its anticodon loop.
[0158] The amino acid sequence of the full-length WRS polypeptide
(or the main splice variant) is shown in SEQ ID NO:5. The amino
acid sequence of the T2-WRS fragment is shown in SEQ ID NO:7, and
the substantially monomeric F260EY201EI278E and F260EY201EH130R
variants of T2-WRS are shown respectively in SEQ ID NOS:8 and 9.
Accordingly, these and other substantially monomeric variants or
fragments of WRS polypeptides may in certain embodiments be
included within the WRS polypeptides of the present invention. As
noted above, however, certain embodiments exclude the specific
T2-WRS polypeptide of SEQ ID NO:7.
[0159] As another exemplary AARS polypeptide, lysyl-tRNA
synthetases (KRS or LysRS) is a member of the class II
aminoacyl-tRNA synthetases, and catalyzes the aminoacylation of
tRNA.sup.lys with lysine, an essential function in protein
synthesis. KRS is an .alpha..sub.2 homodimer that has multiple
ex-aminoacylation functions. For example, KRS interacts with
microphthalmia-associated transcription factor (MITF) and upstream
stimulatory factor (USF2), as part of a mechanism for
transcriptional control of target genes. As another example, KRS is
packaged into the HIV virion via its interaction with the Gag
protein. The HIV packaging of KRS into the virion also includes a
specific cognate tRNA isoacceptor--tRNA.sup.Lys3. Because the
packaged tRNA.sup.Lys3 is the primer for reverse transcription of
the HIV genome, KRS appears to have an important role in the life
cycle of the virus.
[0160] The amino acid sequence of full-length human cytoplasmic KRS
is described in SEQ ID NO:11. Also described is a truncated version
of KRS (SEQ ID NO:11) having residues 70-584 of the full-length
sequence. Certain embodiments include substantially monomeric KRS
polypeptides (e.g., SEQ ID NOS:11, 12) having one or more mutations
or other stabilizing modifications (e.g., chemical modifications
such as pegylation, insertions) within or proximal to (e.g., on the
periphery of) the primary, secondary, or tertiary structure of the
dimer interface of KRS (see FIGS. 18-20). Examples of residues that
lie proximal to or on the surface of the dimer interface include
any one or more of residues E265, 283FIT285, G310, and 539YGLLP543,
their positions being defined by full-length KRS sequence of SEQ ID
NO:11.
[0161] Certain substantially monomeric KRS polypeptides may
comprise one or more insertions, including, for example, insertions
of homologous and/or heterologous polypeptides sequences. Included
are insertions of polypeptides having about 50, 60, 70, 80, 90,
100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220,
230, 250, 250, or more amino acids in length, including all
integers in between. In particular embodiments, an inserted
polypeptide sequence has one or more of the following
characteristics, such as (i) the polypeptide is not derived from a
membrane protein, (ii) the polypeptide has a globular 3D structure,
(iii) the polypeptide has a dimension of about 30-40 .ANG., and/or
(iv) the N-terminus and C-terminus of the polypeptide are located
in close three-dimensional proximity, including any combination of
(i)-(iv). One exemplary polypeptide having all of these
characteristics is the E. coli flavodoxin protein.
[0162] In certain embodiments, the insertion is inserted proximal
to or within the dimer interface. In some embodiments, the
insertion is inserted at the periphery of the dimer interface (see
FIGS. 18-20). The insertion can be inserted proximal to or at
residue G310, as defined by the full-length KRS sequence of SEQ ID
NO:11. An example of a substantially monomeric KRS polypeptide
having the flavodoxin insertion at residue G310 is SEQ ID NO:13,
encoded by the nucleotide sequence of SEQ ID NO:14.
[0163] According to one aspect of the invention, there are provided
substantially monomeric AARS polypeptides having "non-canonical"
activities of therapeutic relevance, as well as compositions
comprising the same. In certain embodiments, the monomeric AARS
polypeptide is a truncated AARS polypeptide, a fragment of an AARS
polypeptide, and/or a variant of an AARS polypeptide. A "truncated"
AARS, as used herein, refers to an AARS protein which is shorter
than its corresponding full-length AARS protein, for example, due
to removal of amino acids from its N- and/or C-terminal ends. The
extent of the truncation, that is, the number of N- and/or
C-terminal amino acid residues removed from a full length AARS
protein can vary considerably while still providing desired
cellular effects when administered to a cell, tissue or subject, as
described herein. In certain embodiments, at least about 5, 10, 15,
20, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, amino
acids, or more, including all intermediate lengths, are truncated
from the N- and/or C-terminus of a full-length mammalian AARS
protein (see, e.g., SEQ ID NOS:1, 5, and 11; and Table A). Specific
examples of naturally-occurring truncated AARS include mini-YRS
(SEQ ID NO:3) and T1-WRS and T2-WRS (SEQ ID NO:7), and a KRS
fragment (SEQ ID NO:12). Intermediate lengths are intended to
include all integers therebetween, for example, 6, 7, 8, etc., 51,
52, 53, etc., 201, 202, 203, etc.
[0164] Variant proteins encompassed by the present application are
substantially monomeric and biologically active, that is, they
continue to possess the "non-canonical" biological activity of a
reference AARS polypeptide sequence (e.g., SEQ ID NOS:4 and 8-9).
Such variants may result from, for example, genetic polymorphism or
from human manipulation. Biologically active variants of a
reference AARS polypeptide fragment will have at least 40%, 50%,
60%, 70%, generally at least 75%, 80%, 85%, usually about 90% to
95% or more, and typically about 98% or more sequence similarity or
identity with the amino acid sequence of a reference protein (e.g.,
Table A) as determined by sequence alignment programs described
elsewhere herein using default parameters. A monomeric and
biologically active variant of a reference AARS polypeptide may
differ from that protein generally by as much 300, 200, 100, 50 or
20 amino acid residues or suitably by as few as 1-15 amino acid
residues, as few as 1-10, such as 6-10, as few as 5, as few as 4,
3, 2, or even 1 amino acid residue. In some embodiments, an AARS
polypeptide differs from the reference sequences in SEQ ID NOS:1,
3-5, 8-9, or 11-13 (or in Table A) by at least one but by less than
15, 10 or 5 amino acid residues. In other embodiments, it differs
from these reference sequences by at least one residue but less
than 20%, 15%, 10% or 5% of the residues.
[0165] A monomeric AARS polypeptide (e.g., SEQ ID NOS:4, 8-9, or
13) may be altered in various ways including amino acid
substitutions, deletions, truncations, and insertions, and still
retain its substantially monomeric form (i.e., it does not
substantially dimerize with itself). In certain embodiments, this
end may be achieved by relying on conservative substitutions and/or
insertions, as described herein.
[0166] Alternatively, an otherwise (predominantly) dimeric AARS
reference polypeptide (e.g., Table A or SEQ ID NOS:1, 3, 5, 7, 11)
may be modified in various ways including amino acid substitutions,
deletions, truncations, and insertions to interfere with its
ability to dimerize, and thereby generate a substantially monomeric
AARS polypeptide. In certain embodiments, this end may be achieved
by relying on selected modifications, such as modifications to the
dimer interface or residues proximal to the dimer interface in the
primary, secondary or tertiary structure of the AARS polypeptide.
Also included are modifications to other domains that contribute to
dimerization.
[0167] Methods for such manipulations are generally known in the
art. For example, amino acid sequence variants of an AARS
polypeptide can be prepared by mutations in the DNA. Methods for
mutagenesis and nucleotide sequence alterations are well known in
the art. See, for example, Kunkel (1985, Proc. Natl. Acad. Sci.
USA. 82: 488-492), Kunkel et al., (1987, Methods in Enzymol, 154:
367-382), U.S. Pat. No. 4,873,192, Watson, J. D. et al.,
("Molecular Biology of the Gene", Fourth Edition,
Benjamin/Cummings, Menlo Park, Calif., 1987) and the references
cited therein. Guidance as to appropriate amino acid substitutions
that do not affect biological activity of the protein of interest
may be found in the model of Dayhoff et al., (1978) Atlas of
Protein Sequence and Structure (Natl. Biomed. Res. Found.,
Washington, D.C.). Methods for screening gene products of
combinatorial libraries made by point mutations or truncation, and
for screening cDNA libraries for gene products having a selected
property are known in the art. Such methods are adaptable for rapid
screening of the gene libraries generated by combinatorial
mutagenesis of AARS polypeptides. Recursive ensemble mutagenesis
(REM), a technique which enhances the frequency of functional
mutants in the libraries, can be used in combination with the
screening assays to identify AARS polypeptide variants (Arkin and
Yourvan (1992) Proc. Natl. Acad. Sci. USA 89: 7811-7815; Delgrave
et al., (1993) Protein Engineering, 6: 327-331). Conservative
substitutions, such as exchanging one amino acid with another
having similar properties, may be desirable as discussed in more
detail below.
[0168] Monomeric and biologically active AARS polypeptides or
fragments thereof may contain conservative amino acid substitutions
at various locations along their sequence, as compared, for
example, to a reference monomeric AARS amino acid sequence (e.g.,
SEQ ID NOS:4, 8-9, or 13). A "conservative amino acid substitution"
is one in which the amino acid residue is replaced with an amino
acid residue having a similar side chain. Families of amino acid
residues having similar side chains have been defined in the art,
which can be generally sub-classified as follows:
[0169] Acidic: The residue has a negative charge due to loss of H
ion at physiological pH and the residue is attracted by aqueous
solution so as to seek the surface positions in the conformation of
a peptide in which it is contained when the peptide is in aqueous
medium at physiological pH. Amino acids having an acidic side chain
include glutamic acid and aspartic acid.
[0170] Basic: The residue has a positive charge due to association
with H ion at physiological pH or within one or two pH units
thereof (e.g., histidine) and the residue is attracted by aqueous
solution so as to seek the surface positions in the conformation of
a peptide in which it is contained when the peptide is in aqueous
medium at physiological pH. Amino acids having a basic side chain
include arginine, lysine and histidine.
[0171] Charged: The residues are charged at physiological pH and,
therefore, include amino acids having acidic or basic side chains
(i.e., glutamic acid, aspartic acid, arginine, lysine and
histidine).
[0172] Hydrophobic: The residues are not charged at physiological
pH and the residue is repelled by aqueous solution so as to seek
the inner positions in the conformation of a peptide in which it is
contained when the peptide is in aqueous medium. Amino acids having
a hydrophobic side chain include tyrosine, valine, isoleucine,
leucine, methionine, phenylalanine and tryptophan.
[0173] Neutral/polar: The residues are not charged at physiological
pH, but the residue is not sufficiently repelled by aqueous
solutions so that it would seek inner positions in the conformation
of a peptide in which it is contained when the peptide is in
aqueous medium. Amino acids having a neutral/polar side chain
include asparagine, glutamine, cysteine, histidine, serine and
threonine.
[0174] In making such changes, the hydropathic index of amino acids
may also be considered. The importance of the hydropathic amino
acid index in conferring interactive biologic function on a protein
is generally understood in the art (Kyte and Doolittle, 1982,
incorporated herein by reference). For example, it is known that
the relative hydropathic character of the amino acid contributes to
the secondary structure of the resultant protein, which in turn
defines the interaction of the protein with other molecules, for
example, enzymes, substrates, receptors, DNA, antibodies, antigens,
and the like. Each amino acid has been assigned a hydropathic index
on the basis of its hydrophobicity and charge characteristics (Kyte
and Doolittle, 1982). These values are: isoleucine (+4.5); valine
(+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cysteine
(+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4);
threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine
(-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5);
glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine
(-3.9); and arginine (-4.5).
[0175] It is known in the art that certain amino acids may be
substituted by other amino acids having a similar hydropathic index
or score and still result in a protein with similar biological
activity, i.e. still obtain a biological functionally equivalent
protein. In making such changes, the substitution of amino acids
whose hydropathic indices are within .+-.2 is preferred, those
within .+-.1 are particularly preferred, and those within .+-.0.5
are even more particularly preferred.
[0176] It is also understood in the art that the substitution of
like amino acids can be made effectively on the basis of
hydrophilicity. As detailed in U.S. Pat. No. 4,554,101, the
following hydrophilicity values have been assigned to amino acid
residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0.+-.1);
glutamate (+3.0.+-.1); serine (+0.3); asparagine (+0.2); glutamine
(+0.2); glycine (0); threonine (-0.4); proline (-0.5.+-.1); alanine
(-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3);
valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3);
phenylalanine (-2.5); tryptophan (-3.4). It is understood that an
amino acid can be substituted for another having a similar
hydrophilicity value and still obtain a biologically equivalent
protein. In such changes, the substitution of amino acids whose
hydrophilicity values are within .+-.2 is preferred, those within
.+-.1 are particularly preferred, and those within .+-.0.5 are even
more particularly preferred.
[0177] This description also characterizes certain amino acids as
"small" since their side chains are not sufficiently large, even if
polar groups are lacking, to confer hydrophobicity. With the
exception of proline, "small" amino acids are those with four
carbons or less when at least one polar group is on the side chain
and three carbons or less when not. Amino acids having a small side
chain include glycine, serine, alanine and threonine. The
gene-encoded secondary amino acid proline is a special case due to
its known effects on the secondary conformation of peptide chains.
The structure of proline differs from all the other
naturally-occurring amino acids in that its side chain is bonded to
the nitrogen of the .alpha.-amino group, as well as the
.alpha.-carbon. Several amino acid similarity matrices are known in
the art (see e.g., PAM120 matrix and PAM250 matrix as disclosed for
example by Dayhoff et al., 1978, A model of evolutionary change in
proteins). Matrices for determining distance relationships In M. O.
Dayhoff, (ed.), Atlas of protein sequence and structure, Vol. 5,
pp. 345-358, National Biomedical Research Foundation, Washington
D.C.; and by Gonnet et al., (Science, 256: 14430-1445, 1992),
however, include proline in the same group as glycine, serine,
alanine and threonine. Accordingly, for the purposes of the present
invention, proline is classified as a "small" amino acid.
[0178] The degree of attraction or repulsion required for
classification as polar or nonpolar is arbitrary and, therefore,
amino acids specifically contemplated by the invention have been
classified as one or the other. Most amino acids not specifically
named can be classified on the basis of known behaviour.
[0179] Amino acid residues can be further sub-classified as cyclic
or non-cyclic, and aromatic or non-aromatic, self-explanatory
classifications with respect to the side-chain substituent groups
of the residues, and as small or large. The residue is considered
small if it contains a total of four carbon atoms or less,
inclusive of the carboxyl carbon, provided an additional polar
substituent is present; three or less if not. Small residues are,
of course, always non-aromatic. Dependent on their structural
properties, amino acid residues may fall in two or more classes.
For the naturally-occurring protein amino acids, sub-classification
according to this scheme is presented in Table B.
TABLE-US-00002 TABLE B Amino acid sub-classification Sub-classes
Amino acids Acidic Aspartic acid, Glutamic acid Basic Noncyclic:
Arginine, Lysine; Cyclic: Histidine Charged Aspartic acid, Glutamic
acid, Arginine, Lysine, Histidine Small Glycine, Serine, Alanine,
Threonine, Proline Polar/neutral Asparagine, Histidine, Glutamine,
Cysteine, Serine, Threonine Polar/large Asparagine, Glutamine
Hydrophobic Tyrosine, Valine, Isoleucine, Leucine, Methionine,
Phenylalanine, Tryptophan Aromatic Tryptophan, Tyrosine,
Phenylalanine Residues Glycine and Proline that influence chain
orientation
[0180] Conservative amino acid substitution also includes groupings
based on side chains. For example, a group of amino acids having
aliphatic side chains is glycine, alanine, valine, leucine, and
isoleucine; a group of amino acids having aliphatic-hydroxyl side
chains is serine and threonine; a group of amino acids having
amide-containing side chains is asparagine and glutamine; a group
of amino acids having aromatic side chains is phenylalanine,
tyrosine, and tryptophan; a group of amino acids having basic side
chains is lysine, arginine, and histidine; and a group of amino
acids having sulphur-containing side chains is cysteine and
methionine. For example, it is reasonable to expect that
replacement of a leucine with an isoleucine or valine, an aspartate
with a glutamate, a threonine with a serine, or a similar
replacement of an amino acid with a structurally related amino acid
will not have a major effect on the properties of the resulting
variant polypeptide. Whether an amino acid change results in a
functional truncated and/or variant AARS polypeptide can readily be
determined by assaying its activity, as described herein (see,
e.g., Examples 2-4). Conservative substitutions are shown in Table
C under the heading of exemplary substitutions. Amino acid
substitutions falling within the scope of the invention, are, in
general, accomplished by selecting substitutions that do not differ
significantly in their effect on maintaining (a) the structure of
the peptide backbone in the area of the substitution, (b) the
charge or hydrophobicity of the molecule at the target site, or (c)
the bulk of the side chain. After the substitutions are introduced,
the variants are screened for biological activity.
TABLE-US-00003 TABLE C Exemplary Amino Acid Substitutions Original
Residue Exemplary Substitutions Preferred Substitutions Ala Val,
Leu, Ile Val Arg Lys, Gln, Asn Lys Asn Gln, His, Lys, Arg Gln Asp
Glu Glu Cys Ser Ser Gln Asn, His, Lys, Asn Glu Asp, Lys Asp Gly Pro
Pro His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met, Ala, Phe, Norleu
Leu Leu Norleu, Ile, Val, Met, Ala, Phe Ile Lys Arg, Gln, Asn Arg
Met Leu, Ile, Phe Leu Phe Leu, Val, Ile, Ala Leu Pro Gly Gly Ser
Thr Thr Thr Ser Ser Trp Tyr Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile,
Leu, Met, Phe, Ala, Norleu Leu
[0181] Alternatively, similar amino acids for making conservative
substitutions can be grouped into three categories based on the
identity of the side chains. The first group includes glutamic
acid, aspartic acid, arginine, lysine, histidine, which all have
charged side chains; the second group includes glycine, serine,
threonine, cysteine, tyrosine, glutamine, asparagine; and the third
group includes leucine, isoleucine, valine, alanine, proline,
phenylalanine, tryptophan, methionine, as described in Zubay, G.,
Biochemistry, third edition, Wm.C. Brown Publishers (1993).
[0182] Thus, a predicted non-essential amino acid residue in a
monomeric AARS polypeptide may be replaced with another amino acid
residue from the same side chain family. Alternatively, mutations
can be introduced randomly along all or part of an AARS coding
sequence, such as by saturation mutagenesis, and the resultant
mutants can be screened for an activity of the parent polypeptide
to identify mutants which retain that activity. Following
mutagenesis of the coding sequences, the encoded peptide can be
expressed recombinantly and the activity of the peptide can be
determined. A "non-essential" amino acid residue is a residue that
can be altered from the reference sequence of an embodiment
polypeptide without abolishing or substantially altering one or
more of its activities. Suitably, the alteration does not
substantially abolish one of these activities, for example, the
activity is at least 20%, 40%, 60%, 70% or 80% 100%, 500%, 1000% or
more of the AARS reference sequence activity (e.g., CXC receptor
agonist activity, angiostatic activity), or its stability as a
monomer under physiological conditions or in solution. An
"essential" amino acid residue is a residue that, when altered from
the sequence a reference AARS polypeptide, results in abolition of
an activity of the parent molecule such that less than 20% of the
reference or non-canonical activity is present. For example, such
essential amino acid residues include those that are conserved in
AARS polypeptides across different species, including those
sequences that are conserved in the active binding site(s) or
motif(s) of AARS polypeptides from various sources.
[0183] As noted above, an otherwise dimeric AARS reference
polypeptide (e.g., SEQ ID NO:1, 3, 5, 7, 11, or the AARS
polypeptides in Table A), or dimerizing fragments or variants
thereof, may be modified in various ways including amino acid
substitutions, deletions, truncations, and insertions to interfere
with its ability to dimerize, and thereby generate a substantially
monomeric AARS polypeptide. Certain embodiments may employ one or
more selective modifications (e.g., mutations, substitutions,
chemical modifications) located in or proximal to the dimer
interface, whether in the primary, secondary, or tertiary structure
of the AARS polypeptide. Exemplary proximal residues include those
that are about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, or 20 residues to the C-terminal or N-terminal side
of the dimer interface of an AARS polypeptide.
[0184] Certain specific embodiments may employ modifications at any
one or more of residues Pro 159, Leu 160, or Leu 161, as in the
full-length YRS or mini-YRS sequence, including combinations
thereof. Also included are modifications to residues that are
proximal to Pro 159, Leu 160, or Leu 161, whether in the primary,
secondary, or tertiary structure of a selected YRS polypeptide.
Certain embodiments include a deletion of Pro 159, Leu 160, and Leu
161. Certain specific embodiments may employ mutations or
substitutions at any one or more of residues F260, Y201, I278,
H130, or E408, as in the full-length WRS or T2-WRS sequence,
including combinations thereof. Also included are modifications to
residues that are proximal to F260, Y201, I278, H130, or E408,
whether in the primary, secondary, or tertiary structure of a
selected WRS polypeptide. Exemplary proximal residues include those
that are about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, or 20 residues relative to the C-terminal or
N-terminal side of either Pro 159, Leu 160, or Leu 161 in a
selected YRS polypeptide, or F260, Y201, I278, H130, or E408 in a
selected WRS polypeptide, or residues E265, 283FIT285, G310, or
539YGLLP543 in a selected KRS polypeptide. The position of these
residues is typically defined by the corresponding full-length AARS
sequence.
[0185] As noted above, certain embodiments include AARS having one
or more insertional stabilizing modifications. As with the other
stabilizing modifications, certain insertions are made within or
proximal to the dimer interface of a selected AARS polypeptide.
Certain insertions can be made at the periphery of the dimer
interface. Included are insertions of homologous or heterologous
polypeptides of about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110,
120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 250,
250, or more amino acids in length, including all integers in
between. In particular embodiments, an inserted polypeptide
sequence has one or more of the following characteristics, such as
(i) the polypeptide is not derived from a membrane protein, (ii)
the polypeptide has a globular 3D structure, (iii) the polypeptide
has a dimension of about 30-40 .ANG., and/or (iv) the N-terminus
and C-terminus of the polypeptide are located in close
three-dimensional proximity, including any combination of
(i)-(iv).
[0186] Accordingly, the present invention contemplates variants of
the naturally-occurring AARS polypeptide sequences or their
biologically-active fragments, wherein the variants are
distinguished from the naturally-occurring sequence by the
addition, deletion, or substitution of one or more amino acid
residues, and wherein such variants or fragments are substantially
monomeric in form. In general, substantially monomeric variants
will display at least about 30, 40, 50, 55, 60, 65, 70, 75, 80, 85,
90, 91, 92, 93, 94, 95, 96, 97, 98, 99% similarity or sequence
identity to a reference AARS polypeptide sequences, for example, as
set forth in SEQ ID NOS:1, 3-5, 7-9, 11-13 or in Table A. Moreover,
sequences differing from the native or parent sequences by the
addition, deletion, or substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80,
90, 100, 110, 120, 130, 140, 150 or more amino acids but which are
substantially monomeric and possess a non-canonical activity that
differs from a dimeric AARS complex are contemplated. In certain
embodiments, the C-terminal or N-terminal region of any of SEQ ID
NOS: 1, 3-5, 7-9, 11-13 or in Table A may be truncated by 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80,
90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250,
300, 350, 400, 450, 500, 550, 600, 650, or 700 or more amino acids,
or by about 10-50, 20-50, 50-100, 100-150, 150-200, 200-250,
250-300, 300-350, 350-400, 400-450, 450-500, 550-600, 600-650,
650-700 or more amino acids, including all integers and ranges in
between (e.g., 101, 102, 103, 104, 105), so long as the truncated
AARS polypeptide is substantially monomeric and retains a
"non-canonical" biological activity, as described herein.
[0187] In some embodiments, variant polypeptides differ from a
reference AARS sequence by at least one but by less than 50, 40,
30, 20, 15, 10, 8, 6, 5, 4, 3 or 2 amino acid residue(s). In other
embodiments, variant polypeptides differ from the corresponding
sequences of SEQ ID NOS: 1, 3-5, 7-9, 11-13 or in Table A by at
least 1% but less than 20%, 15%, 10% or 5% of the residues. (If
this comparison requires alignment, the sequences should be aligned
for maximum similarity. "Looped" out sequences from deletions or
insertions, or mismatches, are considered differences.) In certain
embodiments, the differences include changes at a non-essential
residue or a conservative substitution.
[0188] In certain embodiments, a variant monomeric polypeptide
includes an amino acid sequence having at least about 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94% 95%, 96%,
97%, 98% or more sequence identity or similarity to a corresponding
sequence of an AARS polypeptide as, for example, set forth in SEQ
ID NOS:1, 3-5, 7-9, 11-13 or in Table A, which is substantially
monomeric in form and has the ability to interact with or agonize
CXC receptors such as CXCR-1 and CXCR-2, or has the ability to
interact with VE-cadherin, or reduce angiogenesis, whether in a
subject or in vitro. In relation to the wild-type sequence of human
AARS, certain embodiments may employ one or more selective or
stabilizing mutations to reduce ability of the AARS variant to
dimerize with itself or a second AARS polypeptide.
[0189] Calculations of sequence similarity or sequence identity
between sequences (the terms are used interchangeably herein) are
performed as follows. To determine the percent identity of two
amino acid sequences, or of two nucleic acid sequences, the
sequences are aligned for optimal comparison purposes (e.g., gaps
can be introduced in one or both of a first and a second amino acid
or nucleic acid sequence for optimal alignment and non-homologous
sequences can be disregarded for comparison purposes). In certain
embodiments, the length of a reference sequence aligned for
comparison purposes is at least 30%, preferably at least 40%, more
preferably at least 50%, 60%, and even more preferably at least
70%, 80%, 90%, 100% of the length of the reference sequence. The
amino acid residues or nucleotides at corresponding amino acid
positions or nucleotide positions are then compared. When a
position in the first sequence is occupied by the same amino acid
residue or nucleotide as the corresponding position in the second
sequence, then the molecules are identical at that position.
[0190] The percent identity between the two sequences is a function
of the number of identical positions shared by the sequences,
taking into account the number of gaps, and the length of each gap,
which need to be introduced for optimal alignment of the two
sequences.
[0191] The comparison of sequences and determination of percent
identity between two sequences can be accomplished using a
mathematical algorithm. In a preferred embodiment, the percent
identity between two amino acid sequences is determined using the
Needleman and Wunsch, (1970, J. Mol. Biol. 48: 444-453) algorithm
which has been incorporated into the GAP program in the GCG
software package (available at http://www.gcg.com), using either a
Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14,
12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In
yet another preferred embodiment, the percent identity between two
nucleotide sequences is determined using the GAP program in the GCG
software package (available at http://www.gcg.com), using a
NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and
a length weight of 1, 2, 3, 4, 5, or 6. A particularly preferred
set of parameters (and the one that should be used unless otherwise
specified) are a Blossum 62 scoring matrix with a gap penalty of
12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
The percent identity between two amino acid or nucleotide sequences
can be determined using the algorithm of E. Meyers and W. Miller
(1989, Cabios, 4: 11-17) which has been incorporated into the ALIGN
program (version 2.0), using a PAM120 weight residue table, a gap
length penalty of 12 and a gap penalty of 4.
[0192] The nucleic acid and protein sequences described herein can
be used as a "query sequence" to perform a search against public
databases to, for example, identify other family members or related
sequences. Such searches can be performed using the NBLAST and
XBLAST programs (version 2.0) of Altschul, et al., (1990, J. Mol.
Biol, 215: 403-10). BLAST nucleotide searches can be performed with
the NBLAST program, score=100, wordlength=12 to obtain nucleotide
sequences homologous to nucleic acid molecules of the invention.
BLAST protein searches can be performed with the XBLAST program,
score=50, wordlength=3 to obtain amino acid sequences homologous to
protein molecules of the invention. To obtain gapped alignments for
comparison purposes, Gapped BLAST can be utilized as described in
Altschul et al., (1997, Nucleic Acids Res, 25: 3389-3402). When
utilizing BLAST and Gapped BLAST programs, the default parameters
of the respective programs (e.g., XBLAST and NBLAST) can be
used.
[0193] Variants of an AARS polypeptide can be identified by
screening combinatorial libraries of mutants of an AARS
polypeptide. Libraries or fragments e.g., N terminal, C terminal,
or internal fragments, of AARS protein coding sequence can be used
to generate a variegated population of fragments for screening and
subsequent selection of variants of an AARS polypeptide.
[0194] Methods for screening gene products of combinatorial
libraries made by point mutation or truncation, and for screening
cDNA libraries for gene products having a selected property are
known in the art. Such methods are adaptable for rapid screening of
the gene libraries generated by combinatorial mutagenesis of AARS
polypeptides.
[0195] In certain embodiments of the invention, there are provided
fusion polypeptides, and polynucleotides encoding fusion
polypeptides. Fusion polypeptides refer to polypeptides of the
invention that have been covalently linked, either directly or
indirectly via an amino acid linker, to one or more heterologous
polypeptide sequences (fusion partners). The polypeptides forming
the fusion protein are typically linked C-terminus to N-terminus,
although they can also be linked C-terminus to C-terminus,
N-terminus to N-terminus, or N-terminus to C-terminus. The
polypeptides of the fusion protein can be in any order.
[0196] Fusion proteins include monomeric forms of AARS polypeptides
or polypeptide fragments linked to either another AARS polypeptide
(e.g., to create multiple fragments), to a non-AARS polypeptide, or
to both. A "non-AARS polypeptide" refers to a "heterologous
polypeptide" having an amino acid sequence corresponding to a
protein which is different from an AARS protein, and which is
derived from the same or a different organism. Non-AARS
polypeptides may include different AARS polypeptides. The AARS
polypeptide of the fusion protein can correspond to all or a
portion of a biologically active AARS amino acid sequence. In
certain embodiments, an AARS fusion protein includes at least one
(or two) biologically active portion of an AARS protein.
[0197] The fusion partner may be designed and included for
essentially any desired purpose provided they do not adversely
affect the desired activity of the polypeptide. For example, in one
embodiment, a fusion partner comprises a sequence that assists in
expressing the protein (an expression enhancer) at higher yields
than the native recombinant protein. Other fusion partners may be
selected so as to increase the solubility of the protein or to
enable the protein to be targeted to desired intracellular
compartments. Still further fusion partners include affinity tags,
which facilitate purification of the protein.
[0198] Fusion to heterologous sequences, such as an Fc fragment,
may be utilized to remove unwanted characteristics or to improve
the desired characteristics (e.g., pharmacokinetic properties) of
an AARS polypeptide. For instance, fusion to a heterologous
sequence may increase chemical stability, decrease immunogenicity,
improve in vivo targeting, and/or increase half-life in circulation
of an AARS polypeptide.
[0199] Fusion to heterologous sequences may also be used to create
bi-functional fusion proteins, such as bi-functional proteins that
are not only possess a "non-canonical" AARS biological activity, as
described herein (e.g., CXC receptor agonist activity), but are
also capable of modifying (i.e., stimulating or inhibiting) other
pathways through the heterologous polypeptide. Examples of such
pathways include, but are not limited to, various immune
system-related pathways, such as innate or adaptive immune
activation pathways, or cell-growth or cell-differentiation
regulatory pathways, such as hematopoiesis. In certain aspects, the
heterologous polypeptide may act synergistically with the AARS
polypeptide to regulate a pathway associated with a non-canonical
biological activity. Examples of heterologous polypeptides that may
be utilized to create a bi-functional fusion protein include, but
are not limited to, thrombopoietin, cytokines (e.g., IL-11),
chemokines, and various hematopoietic growth factors, in addition
to biologically active fragments and/or variants thereof.
[0200] Fusion proteins may generally be prepared using standard
techniques. For example, DNA sequences encoding the polypeptide
components of a desired fusion may be assembled separately, and
ligated into an appropriate expression vector. The 3' end of the
DNA sequence encoding one polypeptide component is ligated, with or
without a peptide linker, to the 5' end of a DNA sequence encoding
the second polypeptide component so that the reading frames of the
sequences are in phase. This permits translation into a single
fusion protein that retains the biological activity of both
component polypeptides.
[0201] A peptide linker sequence may be employed to separate the
first and second polypeptide components by a distance sufficient to
ensure that each polypeptide folds into its secondary and tertiary
structures, if desired. Such a peptide linker sequence is
incorporated into the fusion protein using standard techniques well
known in the art. Certain peptide linker sequences may be chosen
based on the following factors: (1) their ability to adopt a
flexible extended conformation; (2) their inability to adopt a
secondary structure that could interact with functional epitopes on
the first and second polypeptides; and (3) the lack of hydrophobic
or charged residues that might react with the polypeptide
functional epitopes. Preferred peptide linker sequences contain
Gly, Asn and Ser residues. Other near neutral amino acids, such as
Thr and Ala may also be used in the linker sequence. Amino acid
sequences which may be usefully employed as linkers include those
disclosed in Maratea et al., Gene 40:39 46 (1985); Murphy et al.,
Proc. Natl. Acad. Sci. USA 83:8258 8262 (1986); U.S. Pat. No.
4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may
generally be from 1 to about 50 amino acids in length. Linker
sequences are not required when the first and second polypeptides
have non-essential N-terminal amino acid regions that can be used
to separate the functional domains and prevent steric
interference.
[0202] The ligated DNA sequences are operably linked to suitable
transcriptional or translational regulatory elements. The
regulatory elements responsible for expression of DNA are located
only 5' to the DNA sequence encoding the first polypeptides.
Similarly, stop codons required to end translation and
transcription termination signals are only present 3' to the DNA
sequence encoding the second polypeptide.
[0203] In general, polypeptides and fusion polypeptides (as well as
their encoding polynucleotides) are isolated. An "isolated"
polypeptide or polynucleotide is one that is removed from its
original environment. For example, a naturally-occurring protein is
isolated if it is separated from some or all of the coexisting
materials in the natural system. Preferably, such polypeptides are
at least about 90% pure, more preferably at least about 95% pure
and most preferably at least about 99% pure. A polynucleotide is
considered to be isolated if, for example, it is cloned into a
vector that is not a part of the natural environment.
[0204] In other embodiments, an AARS polypeptide of the invention
may be part of a multi-unit complex. A multi-unit complex of the
present invention can include, for example, at least 2, 3, 4, or 5
or more monomers. The monomers and/or multi-unit complexes of the
present invention may be soluble and may be isolated or purified to
homogeneity. Monomer units of a multi-unit complex may be
different, homologous, substantially homologous, or identical to
one another. However, a multi-unit complex of the invention
includes at least one monomer comprising an AARS polypeptide as
described herein or, in other embodiments, at least two or more
AARS polypeptides as described herein.
[0205] Covalently linked monomers can be linked directly (by bonds)
or indirectly (e.g., via a linker). For directly linking the
polypeptide monomers herein, it may be beneficial to modify the
polypeptides herein to enhance dimerization. For example, one or
more amino acid residues of an AARS polypeptide may be modified by
the addition or substation by one or more cysteines. Methods for
creating amino acid substitutions, such as cysteine substitutions,
or other modifications to facilitate linking, are well known to
those skilled in the art.
[0206] Certain embodiments of the present invention also
contemplate the use of modified AARS polypeptides, including
modifications that improve desired characteristics of an AARS
polypeptide, as described herein. Illustrative modifications of
AARS polypeptides of the invention include, but are not limited to,
chemical and/or enzymatic derivatizations at one or more
constituent amino acids, including side chain modifications,
backbone modifications, and N- and C-terminal modifications
including acetylation, hydroxylation, methylation, glycosylation
(e.g., N-linked, O-linked), amidation, and the attachment of
carbohydrate or lipid moieties, cofactors, and the like. Exemplary
modifications also include pegylation of an AARS polypeptide (see,
e.g., Veronese and Harris, Advanced Drug Delivery Reviews 54:
453-456, 2002, herein incorporated by reference).
[0207] In certain aspects, chemoselective ligation technology may
be utilized to modify AARS polypeptides of the invention, such as
by attaching polymers in a site-specific and controlled manner.
Such technology typically relies on the incorporation of
chemoselective anchors into the protein backbone by either chemical
or recombinant means and subsequent modification with a polymer
carrying a complementary linker. As a result, the assembly process
and the covalent structure of the resulting protein-polymer
conjugate may be controlled, enabling the rational optimization of
drug properties, such as efficacy and pharmacokinetic properties
(see, e.g., Kochendoerfer, Current Opinion in Chemical Biology
9:555-560, 2005).
[0208] In certain embodiments, these and other forms of chemical
modification may be used to generate a substantially monomeric AARS
polypeptide, such as by interfering with the dimer interface or
other structural feature required for dimerization (see, e.g., FIG.
1). For instance, certain embodiments may incorporate at least one
stabilizing modification by chemically modifying (e.g., pegylation)
one or more selected residues within or proximal to the dimer
interface of the full-length AARS polypeptide, or a fragment
thereof, to prevent or reduce the ability of the AARS polypeptide
to dimerize with itself or with a second AARS polypeptide. Merely
by way of illustration, residues located within the dimer interface
or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18,
19, 20 to the C-terminal or N-terminal side of the dimer interface,
or residues proximal in the secondary or tertiary structure of the
dimer interface, may be chemically modified, or may be first
mutated to an appropriate residue (e.g., a residue that better
accepts pegylation or glycosylation) and then chemically
modified.
[0209] For YRS, any one or more of residues 159-161 (or their
nearby residues, including residues within 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, or more residues of 159-161, or residues proximal in the
primary, secondary, or tertiary structure of YRS) may be chemically
modified, or may be first mutated to an appropriate residue (e.g.,
a residue that better accepts pegylation or glycosylation) and then
chemically modified. For WRS, any one or more of residues F260,
Y201, I278, H130, or E408 (or their nearby residues, including
residues within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more residues of
F260, Y201, I278, H130, or E408, or residues proximal in the
primary, secondary, or tertiary structure of WRS) may be chemically
modified, or may be first mutated to an appropriate residue (e.g.,
a residue that better accepts pegylation) and then chemically
modified.
[0210] In certain embodiments, the AARS polypeptides of the present
invention may specifically include or specifically exclude any one
or more of the structural and/or functional features described
herein.
[0211] The substantially monomeric AARS polypeptides of the
invention may be prepared by any suitable procedure known to those
of skill in the art, such as by recombinant techniques. For
example, AARS polypeptides may be prepared by a procedure including
the steps of: (a) preparing a construct comprising a polynucleotide
sequence that encodes an AARS polypeptide and that is operably
linked to a regulatory element; (b) introducing the construct into
a host cell; (c) culturing the host cell to express the AARS
polypeptide; and (d) isolating the AARS polypeptide from the host
cell. Recombinant AARS polypeptides can be conveniently prepared
using standard protocols as described for example in Sambrook, et
al., (1989, supra), in particular Sections 16 and 17; Ausubel et
al., (1994, supra), in particular Chapters 10 and 16; and Coligan
et al., Current Protocols in Protein Science (John Wiley &
Sons, Inc. 1995-1997), in particular Chapters 1, 5 and 6.
[0212] In addition to recombinant production methods, polypeptides
of the invention, and fragments thereof, may be produced by direct
peptide synthesis using solid-phase techniques (Merrifield, J. Am.
Chem. Soc. 85:2149-2154 (1963)). Protein synthesis may be performed
using manual techniques or by automation. Automated synthesis may
be achieved, for example, using Applied Biosystems 431A Peptide
Synthesizer (Perkin Elmer). Alternatively, various fragments may be
chemically synthesized separately and combined using chemical
methods to produce the desired molecule.
Polynucleotide Compositions
[0213] The present invention also provides isolated polynucleotides
that encode the AARS polypeptides of the invention, as well as
compositions comprising such polynucleotides.
[0214] As used herein, the terms "DNA" and "polynucleotide" and
"nucleic acid" refer to a DNA molecule that has been isolated free
of total genomic DNA of a particular species. Therefore, a DNA
segment encoding a polypeptide refers to a DNA segment that
contains one or more coding sequences yet is substantially isolated
away from, or purified free from, total genomic DNA of the species
from which the DNA segment is obtained. Included within the terms
"DNA segment" and "polynucleotide" are DNA segments and smaller
fragments of such segments, and also recombinant vectors,
including, for example, plasmids, cosmids, phagemids, phage,
viruses, and the like.
[0215] As will be understood by those skilled in the art, the
polynucleotide sequences of this invention can include genomic
sequences, extra-genomic and plasmid-encoded sequences and smaller
engineered gene segments that express, or may be adapted to
express, proteins, polypeptides, peptides and the like. Such
segments may be naturally isolated, or modified synthetically by
the hand of man.
[0216] As will be recognized by the skilled artisan,
polynucleotides may be single-stranded (coding or antisense) or
double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA
molecules. Additional coding or non-coding sequences may, but need
not, be present within a polynucleotide of the present invention,
and a polynucleotide may, but need not, be linked to other
molecules and/or support materials.
[0217] Polynucleotides may comprise a native sequence (i.e., an
endogenous sequence that encodes an AARS or a portion thereof) or
may comprise a variant, or a biological functional equivalent of
such a sequence. Polynucleotide variants may contain one or more
substitutions, additions, deletions and/or insertions, as further
described below, preferably such that the desired activity of the
encoded polypeptide is not substantially diminished relative to the
unmodified polypeptide. The effect on the activity of the encoded
polypeptide may generally be assessed as described herein.
[0218] In additional embodiments, the present invention provides
isolated polynucleotides comprising various lengths of contiguous
stretches of sequence identical to or complementary to an AARS,
wherein the isolated polynucleotides encode an AARS as described
herein. Exemplary nucleotide sequences that encode the AARS
polypeptides of the application encompass coding sequences, such as
the polynucleotide sequence of SEQ ID NO:2 or 6 or 14 (or the
coding sequences of the AARS polypeptides in Table A, including
monomeric variants thereof), as well as portions of the full-length
or substantially full-length nucleotide sequences of the AARS genes
or their transcripts or DNA copies of these transcripts.
[0219] Portions of an AARS nucleotide sequence may encode
polypeptide portions or segments that retain the non-canonical
biological activity of the reference polypeptide, including for
illustrative purposes the polypeptide of SEQ ID NOS:4, 8-9, or 13.
A portion of an AARS nucleotide sequence that encodes a
biologically active fragment of an AARS polypeptide may encode at
least about 20, 21, 22, 23, 24, 25, 30, 40, 50, 60, 70, 80, 90,
100, 120, 150, 300, 400, 450 or more contiguous amino acid
residues, or almost up to the total number of amino acids present
in a full-length AARS polypeptide, as well as intermediate lengths,
as long as it encodes a substantially monomeric form of an AARS
polypeptide. It will be readily understood that "intermediate
lengths," in this context and in all other contexts used herein,
means any length between the quoted values, such as 101, 102, 103,
etc.; 151, 152, 153, etc.; 201, 202, 203, etc.
[0220] The invention also contemplates variants of the AARS
nucleotide sequences. Nucleic acid variants can be
naturally-occurring, such as allelic variants (same locus),
homologs (different locus), and orthologs (different organism) or
can be non naturally-occurring. Naturally occurring variants such
as these can be identified with the use of well-known molecular
biology techniques, as, for example, with polymerase chain reaction
(PCR) and hybridization techniques as known in the art.
Non-naturally occurring variants can be made by mutagenesis
techniques, including those applied to polynucleotides, cells, or
organisms. The variants can contain nucleotide substitutions,
deletions, inversions and insertions. Variation can occur in either
or both the coding and non-coding regions. The variations can
produce both conservative and non-conservative amino acid
substitutions (as compared in the encoded product). For nucleotide
sequences, conservative variants include those sequences that,
because of the degeneracy of the genetic code, encode the amino
acid sequence of a reference AARS polypeptide, such as the
sequences set forth in SEQ ID NO:2 and 6 or 14. Variant nucleotide
sequences also include synthetically derived nucleotide sequences,
such as those generated, for example, by using site-directed
mutagenesis but which still encode a monomeric AARS polypeptide, as
described herein. Generally, variants of a particular monomeric
AARS nucleotide sequence may have at least about 30%, 40% 50%, 55%,
60%, 65%, 70%, generally at least about 75%, 80%, 85%, desirably
about 90% to 95% or more, and more suitably about 98% or more
sequence identity to that particular nucleotide sequence as
determined by sequence alignment programs described elsewhere
herein using default parameters.
[0221] AARS nucleotide sequences can be used to isolate
corresponding sequences and alleles from other organisms,
particularly other organisms or microorganisms. Methods are readily
available in the art for the hybridization of nucleic acid
sequences. Coding sequences from other organisms may be isolated
according to well known techniques based on their sequence identity
with the coding sequences set forth herein. In these techniques all
or part of the known coding sequence is used as a probe which
selectively hybridizes to other AARS-coding sequences present in a
population of cloned genomic DNA fragments or cDNA fragments (i.e.,
genomic or cDNA libraries) from a chosen organism.
[0222] Accordingly, the present invention also contemplates
polynucleotides that hybridize to reference AARS nucleotide
sequences, or to their complements, under stringency conditions
described below. As used herein, the term "hybridizes under low
stringency, medium stringency, high stringency, or very high
stringency conditions" describes conditions for hybridization and
washing. Guidance for performing hybridization reactions can be
found in Ausubel et al., (1998, supra), Sections 6.3.1-6.3.6.
Aqueous and non-aqueous methods are described in that reference and
either can be used. Reference herein to low stringency conditions
include and encompass from at least about 1% v/v to at least about
15% v/v formamide and from at least about 1 M to at least about 2 M
salt for hybridization at 42.degree. C., and at least about 1 M to
at least about 2 M salt for washing at 42.degree. C. Low stringency
conditions also may include 1% Bovine Serum Albumin (BSA), 1 mM
EDTA, 0.5 M NaHPO.sub.4 (pH 7.2), 7% SDS for hybridization at
65.degree. C., and (i) 2.times.SSC, 0.1% SDS; or (ii) 0.5% BSA, 1
mM EDTA, 40 mM NaHPO.sub.4 (pH 7.2), 5% SDS for washing at room
temperature. One embodiment of low stringency conditions includes
hybridization in 6.times.sodium chloride/sodium citrate (SSC) at
about 45.degree..quadrature.C., followed by two washes in
0.2.times.SSC, 0.1% SDS at least at 50.degree. C. (the temperature
of the washes can be increased to 55.degree. C. for low stringency
conditions). Medium stringency conditions include and encompass
from at least about 16% v/v to at least about 30% v/v formamide and
from at least about 0.5 M to at least about 0.9 M salt for
hybridization at 42.degree. C., and at least about 0.1 M to at
least about 0.2 M salt for washing at 55.degree. C. Medium
stringency conditions also may include 1% Bovine Serum Albumin
(BSA), 1 mM EDTA, 0.5 M NaHPO.sub.4 (pH 7.2), 7% SDS for
hybridization at 65.degree. C., and (i) 2.times.SSC, 0.1% SDS; or
(ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO.sub.4 (pH 7.2), 5% SDS for
washing at 60-65.degree. C. One embodiment of medium stringency
conditions includes hybridizing in 6.times.SSC at about
45.degree..quadrature.C., followed by one or more washes in
0.2.times.SSC, 0.1% SDS at 60.degree. C. High stringency conditions
include and encompass from at least about 31% v/v to at least about
50% v/v formamide and from about 0.01 M to about 0.15 M salt for
hybridization at 42.degree. C., and about 0.01 M to about 0.02 M
salt for washing at 55.degree. C. High stringency conditions also
may include 1% BSA, 1 mM EDTA, 0.5 M NaHPO.sub.4 (pH 7.2), 7% SDS
for hybridization at 65.degree. C., and (i) 0.2.times.SSC, 0.1%
SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO.sub.4 (pH 7.2), 1%
SDS for washing at a temperature in excess of 65.degree. C. One
embodiment of high stringency conditions includes hybridizing in
6.times.SSC at about 45.degree. C., followed by one or more washes
in 0.2.times.SSC, 0.1% SDS at 65.degree. C.
[0223] In certain embodiments, an AARS polypeptide is encoded by a
polynucleotide that hybridizes to a disclosed nucleotide sequence
under very high stringency conditions. One embodiment of very high
stringency conditions includes hybridizing in 0.5 M sodium
phosphate, 7% SDS at 65.degree. C., followed by one or more washes
in 0.2.times.SSC, 1% SDS at 65.degree. C.
[0224] Other stringency conditions are well known in the art and a
skilled addressee will recognize that various factors can be
manipulated to optimize the specificity of the hybridization.
Optimization of the stringency of the final washes can serve to
ensure a high degree of hybridization. For detailed examples, see
Ausubel et al., supra at pages 2.10.1 to 2.10.16 and Sambrook et
al. (1989, supra) at sections 1.101 to 1.104.
[0225] While stringent washes are typically carried out at
temperatures from about 42.degree. C. to 68.degree. C., one skilled
in the art will appreciate that other temperatures may be suitable
for stringent conditions. Maximum hybridization rate typically
occurs at about 20.degree. C. to 25.degree. C. below the T.sub.m
for formation of a DNA-DNA hybrid. It is well known in the art that
the T.sub.m is the melting temperature, or temperature at which two
complementary polynucleotide sequences dissociate. Methods for
estimating T.sub.m are well known in the art (see Ausubel et al.,
supra at page 2.10.8).
[0226] In general, the T.sub.m of a perfectly matched duplex of DNA
may be predicted as an approximation by the formula:
T.sub.m=81.5+16.6 (log.sub.10 M)+0.41 (% G+C)-0.63 (%
formamide)-(600/length) wherein: M is the concentration of
Na.sup.+, preferably in the range of 0.01 molar to 0.4 molar; % G+C
is the sum of guanosine and cytosine bases as a percentage of the
total number of bases, within the range between 30% and 75% G+C; %
formamide is the percent formamide concentration by volume; length
is the number of base pairs in the DNA duplex. The T.sub.m of a
duplex DNA decreases by approximately 1.degree. C. with every
increase of 1% in the number of randomly mismatched base pairs.
Washing is generally carried out at T.sub.m-15.degree. C. for high
stringency, or T.sub.m-30.degree. C. for moderate stringency.
[0227] In one example of a hybridization procedure, a membrane
(e.g., a nitrocellulose membrane or a nylon membrane) containing
immobilized DNA is hybridized overnight at 42.degree. C. in a
hybridization buffer (50% deionized formamide, 5.times.SSC,
5.times.Denhardt's solution (0.1% ficoll, 0.1% polyvinylpyrollidone
and 0.1% bovine serum albumin), 0.1% SDS and 200 mg/mL denatured
salmon sperm DNA) containing a labeled probe. The membrane is then
subjected to two sequential medium stringency washes (i.e.,
2.times.SSC, 0.1% SDS for 15 min at 45.degree. C., followed by
2.times.SSC, 0.1% SDS for 15 min at 50.degree. C.), followed by two
sequential higher stringency washes (i.e., 0.2.times.SSC, 0.1% SDS
for 12 min at 55.degree. C. followed by 0.2.times.SSC and 0.1% SDS
solution for 12 min at 65-68.degree. C.
[0228] Moreover, it will be appreciated by those of ordinary skill
in the art that, as a result of the degeneracy of the genetic code,
there are many nucleotide sequences that encode a polypeptide as
described herein. Some of these polynucleotides bear minimal
homology to the nucleotide sequence of any native gene.
Nonetheless, polynucleotides that vary due to differences in codon
usage are specifically contemplated by the present invention, for
example polynucleotides that are optimized for human and/or primate
codon selection. Further, alleles of the genes comprising the
polynucleotide sequences provided herein are within the scope of
the present invention. Alleles are endogenous genes that are
altered as a result of one or more mutations, such as deletions,
additions and/or substitutions of nucleotides. The resulting mRNA
and protein may, but need not, have an altered structure or
function. Alleles may be identified using standard techniques (such
as hybridization, amplification and/or database sequence
comparison).
[0229] The polynucleotides of the present invention, regardless of
the length of the coding sequence itself, may be combined with
other DNA sequences, such as promoters, polyadenylation signals,
additional restriction enzyme sites, multiple cloning sites, other
coding segments, and the like, such that their overall length may
vary considerably. It is therefore contemplated that a
polynucleotide fragment of almost any length may be employed; with
the total length preferably being limited by the ease of
preparation and use in the intended recombinant DNA protocol.
[0230] Polynucleotides and fusions thereof may be prepared,
manipulated and/or expressed using any of a variety of well
established techniques known and available in the art. For example,
polynucleotide sequences which encode polypeptides of the
invention, or fusion proteins or functional equivalents thereof,
may be used in recombinant DNA molecules to direct expression of an
AARS polypeptide in appropriate host cells. Due to the inherent
degeneracy of the genetic code, other DNA sequences that encode
substantially the same or a functionally equivalent amino acid
sequence may be produced and these sequences may be used to clone
and express a given polypeptide.
[0231] As will be understood by those of skill in the art, it may
be advantageous in some instances to produce polypeptide-encoding
nucleotide sequences possessing non-naturally occurring codons. For
example, codons preferred by a particular prokaryotic or eukaryotic
host can be selected to increase the rate of protein expression or
to produce a recombinant RNA transcript having desirable
properties, such as a half-life which is longer than that of a
transcript generated from the naturally occurring sequence.
[0232] Moreover, the polynucleotide sequences of the present
invention can be engineered using methods generally known in the
art in order to alter polypeptide encoding sequences for a variety
of reasons, including but not limited to, alterations which modify
the cloning, processing, expression and/or activity of the gene
product.
[0233] In order to express a desired polypeptide, a nucleotide
sequence encoding the polypeptide, or a functional equivalent, may
be inserted into appropriate expression vector, i.e., a vector
which contains the necessary elements for the transcription and
translation of the inserted coding sequence. Methods which are well
known to those skilled in the art may be used to construct
expression vectors containing sequences encoding a polypeptide of
interest and appropriate transcriptional and translational control
elements. These methods include in vitro recombinant DNA
techniques, synthetic techniques, and in vivo genetic
recombination. Such techniques are described in Sambrook et al.,
Molecular Cloning, A Laboratory Manual (1989), and Ausubel et al.,
Current Protocols in Molecular Biology (1989).
[0234] A variety of expression vector/host systems are known and
may be utilized to contain and express polynucleotide sequences.
These include, but are not limited to, microorganisms such as
bacteria transformed with recombinant bacteriophage, plasmid, or
cosmid DNA expression vectors; yeast transformed with yeast
expression vectors; insect cell systems infected with virus
expression vectors (e.g., baculovirus); plant cell systems
transformed with virus expression vectors (e.g., cauliflower mosaic
virus, CaMV; tobacco mosaic virus, TMV) or with bacterial
expression vectors (e.g., Ti or pBR322 plasmids); or animal cell
systems.
[0235] The "control elements" or "regulatory sequences" present in
an expression vector are those non-translated regions of the
vector--enhancers, promoters, 5' and 3' untranslated regions--which
interact with host cellular proteins to carry out transcription and
translation. Such elements may vary in their strength and
specificity. Depending on the vector system and host utilized, any
number of suitable transcription and translation elements,
including constitutive and inducible promoters, may be used. For
example, when cloning in bacterial systems, inducible promoters
such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid
(Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL,
Gaithersburg, Md.) and the like may be used. In mammalian cell
systems, promoters from mammalian genes or from mammalian viruses
are generally preferred. If it is necessary to generate a cell line
that contains multiple copies of the sequence encoding a
polypeptide, vectors based on SV40 or EBV may be advantageously
used with an appropriate selectable marker.
[0236] In bacterial systems, a number of expression vectors may be
selected depending upon the use intended for the expressed
polypeptide. For example, when large quantities are needed, vectors
which direct high level expression of fusion proteins that are
readily purified may be used. Such vectors include, but are not
limited to, the multifunctional E. coli cloning and expression
vectors such as BLUESCRIPT (Stratagene), in which the sequence
encoding the polypeptide of interest may be ligated into the vector
in frame with sequences for the amino-terminal Met and the
subsequent 7 residues of .beta.-galactosidase so that a hybrid
protein is produced; pIN vectors (Van Heeke & Schuster, J.
Biol. Chem. 264:5503 5509 (1989)); and the like. pGEX Vectors
(Promega, Madison, Wis.) may also be used to express foreign
polypeptides as fusion proteins with glutathione S-transferase
(GST). In general, such fusion proteins are soluble and can easily
be purified from lysed cells by adsorption to glutathione-agarose
beads followed by elution in the presence of free glutathione.
Proteins made in such systems may be designed to include heparin,
thrombin, or factor XA protease cleavage sites so that the cloned
polypeptide of interest can be released from the GST moiety at
will.
[0237] In the yeast, Saccharomyces cerevisiae, a number of vectors
containing constitutive or inducible promoters such as alpha
factor, alcohol oxidase, and PGH may be used. For reviews, see
Ausubel et al. (supra) and Grant et al., Methods Enzymol.
153:516-544 (1987).
[0238] In cases where plant expression vectors are used, the
expression of sequences encoding polypeptides may be driven by any
of a number of promoters. For example, viral promoters such as the
35S and 19S promoters of CaMV may be used alone or in combination
with the omega leader sequence from TMV (Takamatsu, EMBO J.
6:307-311 (1987)). Alternatively, plant promoters such as the small
subunit of RUBISCO or heat shock promoters may be used (Coruzzi et
al., EMBO J. 3:1671-1680 (1984); Broglie et al., Science
224:838-843 (1984); and Winter et al., Results Probl. Cell Differ.
17:85-105 (1991)). These constructs can be introduced into plant
cells by direct DNA transformation or pathogen-mediated
transfection. Such techniques are described in a number of
generally available reviews (see, e.g., Hobbs in McGraw Hill,
Yearbook of Science and Technology, pp. 191-196 (1992)).
[0239] An insect system may also be used to express a polypeptide
of interest. For example, in one such system, Autographa
californica nuclear polyhedrosis virus (AcNPV) is used as a vector
to express foreign genes in Spodoptera frugiperda cells or in
Trichoplusia larvae. The sequences encoding the polypeptide may be
cloned into a non-essential region of the virus, such as the
polyhedrin gene, and placed under control of the polyhedrin
promoter. Successful insertion of the polypeptide-encoding sequence
will render the polyhedrin gene inactive and produce recombinant
virus lacking coat protein. The recombinant viruses may then be
used to infect, for example, S. frugiperda cells or Trichoplusia
larvae in which the polypeptide of interest may be expressed
(Engelhard et al., Proc. Natl. Acad. Sci. U.S.A. 91:3224-3227
(1994)).
[0240] In mammalian host cells, a number of viral-based expression
systems are generally available. For example, in cases where an
adenovirus is used as an expression vector, sequences encoding a
polypeptide of interest may be ligated into an adenovirus
transcription/translation complex consisting of the late promoter
and tripartite leader sequence. Insertion in a non-essential E1 or
E3 region of the viral genome may be used to obtain a viable virus
which is capable of expressing the polypeptide in infected host
cells (Logan & Shenk, Proc. Natl. Acad. Sci. U.S.A.
81:3655-3659 (1984)). In addition, transcription enhancers, such as
the Rous sarcoma virus (RSV) enhancer, may be used to increase
expression in mammalian host cells.
[0241] Specific initiation signals may also be used to achieve more
efficient translation of sequences encoding a polypeptide of
interest. Such signals include the ATG initiation codon and
adjacent sequences. In cases where sequences encoding the
polypeptide, its initiation codon, and upstream sequences are
inserted into the appropriate expression vector, no additional
transcriptional or translational control signals may be needed.
However, in cases where only coding sequence, or a portion thereof,
is inserted, exogenous translational control signals including the
ATG initiation codon should be provided. Furthermore, the
initiation codon should be in the correct reading frame to ensure
translation of the entire insert. Exogenous translational elements
and initiation codons may be of various origins, both natural and
synthetic. The efficiency of expression may be enhanced by the
inclusion of enhancers which are appropriate for the particular
cell system which is used, such as those described in the
literature (Scharf. et al., Results Probl. Cell Differ. 20:125-162
(1994)).
[0242] In addition, a host cell strain may be chosen for its
ability to modulate the expression of the inserted sequences or to
process the expressed protein in the desired fashion. Such
modifications of the polypeptide include, but are not limited to,
acetylation, carboxylation, glycosylation, phosphorylation,
lipidation, and acylation. Post-translational processing which
cleaves a "prepro" form of the protein may also be used to
facilitate correct insertion, folding and/or function. Different
host cells such as CHO, HeLa, MDCK, HEK293, and W138, which have
specific cellular machinery and characteristic mechanisms for such
post-translational activities, may be chosen to ensure the correct
modification and processing of the foreign protein.
[0243] For long-term, high-yield production of recombinant
proteins, stable expression is generally preferred. For example,
cell lines which stably express a polynucleotide of interest may be
transformed using expression vectors which may contain viral
origins of replication and/or endogenous expression elements and a
selectable marker gene on the same or on a separate vector.
Following the introduction of the vector, cells may be allowed to
grow for 1-2 days in an enriched media before they are switched to
selective media. The purpose of the selectable marker is to confer
resistance to selection, and its presence allows growth and
recovery of cells which successfully express the introduced
sequences. Resistant clones of stably transformed cells may be
proliferated using tissue culture techniques appropriate to the
cell type.
[0244] Any number of selection systems may be used to recover
transformed cell lines. These include, but are not limited to, the
herpes simplex virus thymidine kinase (Wigler et al., Cell 11:
223-232 (1977)) and adenine phosphoribosyltransferase (Lowy et al.,
Cell 22:817-823 (1990)) genes which can be employed in tk- or aprt-
cells, respectively. Also, antimetabolite, antibiotic or herbicide
resistance can be used as the basis for selection; for example,
dhfr which confers resistance to methotrexate (Wigler et al., Proc.
Natl. Acad. Sci. U.S.A. 77:3567-70 (1980)); npt, which confers
resistance to the aminoglycosides, neomycin and G-418
(Colbere-Garapin et al., J. Mol. Biol. 150:1-14 (1981)); and als or
pat, which confer resistance to chlorsulfuron and phosphinotricin
acetyltransferase, respectively (Murry, supra). Additional
selectable genes have been described, for example, trpB, which
allows cells to utilize indole in place of tryptophan, or hisD,
which allows cells to utilize histinol in place of histidine
(Hartman & Mulligan, Proc. Natl. Acad. Sci. U.S.A. 85:8047-51
(1988)). The use of visible markers has gained popularity with such
markers as anthocyanins, .beta.-glucuronidase and its substrate
GUS, and luciferase and its substrate luciferin, being widely used
not only to identify transformants, but also to quantify the amount
of transient or stable protein expression attributable to a
specific vector system (Rhodes et al., Methods Mol. Biol.
55:121-131 (1995)).
[0245] A variety of protocols for detecting and measuring the
expression of polynucleotide-encoded products, using either
polyclonal or monoclonal antibodies specific for the product are
known in the art. Examples include enzyme-linked immunosorbent
assay (ELISA), radioimmunoassay (RIA), and fluorescence activated
cell sorting (FACS). These and other assays are described, among
other places, in Hampton et al., Serological Methods, a Laboratory
Manual (1990) and Maddox et al., J. Exp. Med. 158:1211-1216
(1983).
[0246] A wide variety of labels and conjugation techniques are
known by those skilled in the art and may be used in various
nucleic acid and amino acid assays. Means for producing labeled
hybridization or PCR probes for detecting sequences related to
polynucleotides include oligolabeling, nick translation,
end-labeling or PCR amplification using a labeled nucleotide.
Alternatively, the sequences, or any portions thereof may be cloned
into a vector for the production of an mRNA probe. 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, T3, or SP6 and labeled nucleotides. These
procedures may be conducted using a variety of commercially
available kits. Suitable reporter molecules or labels, which may be
used include radionuclides, enzymes, fluorescent, chemiluminescent,
or chromogenic agents as well as substrates, cofactors, inhibitors,
magnetic particles, and the like.
[0247] Host cells transformed with a polynucleotide sequence of
interest may be cultured under conditions suitable for the
expression and recovery of the protein from cell culture. The
protein produced by a recombinant cell may be secreted or contained
intracellularly depending on the sequence and/or the vector used.
As will be understood by those of skill in the art, expression
vectors containing polynucleotides of the invention may be designed
to contain signal sequences which direct secretion of the encoded
polypeptide through a prokaryotic or eukaryotic cell membrane.
Other recombinant constructions may be used to join sequences
encoding a polypeptide of interest to nucleotide sequence encoding
a polypeptide domain which will facilitate purification of soluble
proteins.
[0248] In addition to recombinant production methods, polypeptides
of the invention, and fragments thereof, may be produced by direct
peptide synthesis using solid-phase techniques (Merrifield, J. Am.
Chem. Soc. 85:2149-2154 (1963)). Protein synthesis may be performed
using manual techniques or by automation. Automated synthesis may
be achieved, for example, using Applied Biosystems 431A Peptide
Synthesizer (Perkin Elmer). Alternatively, various fragments may be
chemically synthesized separately and combined using chemical
methods to produce the full length molecule.
[0249] According to another aspect of the invention,
polynucleotides encoding polypeptides of the invention may be
delivered to a subject in vivo, e.g., using gene therapy
techniques. Gene therapy refers generally to the transfer of
heterologous nucleic acids to the certain cells, target cells, of a
mammal, particularly a human, with a disorder or conditions for
which such therapy is sought. The nucleic acid is introduced into
the selected target cells in a manner such that the heterologous
DNA is expressed and a therapeutic product encoded thereby is
produced.
[0250] Various viral vectors that can be utilized for gene therapy
as taught herein include adenovirus, herpes virus, vaccinia,
adeno-associated virus (AAV), or, preferably, an RNA virus such as
a retrovirus. Preferably, the retroviral vector is a derivative of
a murine or avian retrovirus, or is a lentiviral vector. The
preferred retroviral vector is a lentiviral vector. Examples of
retroviral vectors in which a single foreign gene can be inserted
include, but are not limited to: Moloney murine leukemia virus
(MoMuLV), Harvey murine sarcoma virus (HaMuSV), murine mammary
tumor virus (MuMTV), SIV, BIV, HIV and Rous Sarcoma Virus (RSV). A
number of additional retroviral vectors can incorporate multiple
genes. All of these vectors can transfer or incorporate a gene for
a selectable marker so that transduced cells can be identified and
generated. By inserting a zinc finger derived-DNA binding
polypeptide sequence of interest into the viral vector, along with
another gene that encodes the ligand for a receptor on a specific
target cell, for example, the vector may be made target specific.
Retroviral vectors can be made target specific by inserting, for
example, a polynucleotide encoding a protein (dimer). Illustrative
targeting may be accomplished by using an antibody to target the
retroviral vector. Those of skill in the art will know of, or can
readily ascertain without undue experimentation, specific
polynucleotide sequences which can be inserted into the retroviral
genome to allow target specific delivery of the retroviral vector
containing the zinc finger-nucleotide binding protein
polynucleotide.
[0251] Since recombinant retroviruses are defective, they require
assistance in order to produce infectious vector particles. This
assistance can be provided, for example, by using helper cell lines
that contain plasmids encoding all of the structural genes of the
retrovirus under the control of regulatory sequences within the
LTR. These plasmids are missing a nucleotide sequence which enables
the packaging mechanism to recognize an RNA transcript for
encapsulation. Helper cell lines which have deletions of the
packaging signal include but are not limited to .PSI.2, PA317 and
PA12, for example. These cell lines produce empty virions, since no
genome is packaged. If a retroviral vector is introduced into such
cells in which the packaging signal is intact, but the structural
genes are replaced by other genes of interest, the vector can be
packaged and vector virion produced. The vector virions produced by
this method can then be used to infect a tissue cell line, such as
NIH 3T3 cells, to produce large quantities of chimeric retroviral
virions.
[0252] "Non-viral" delivery techniques for gene therapy can also be
used including, for example, DNA-ligand complexes,
adenovirus-ligand-DNA complexes, direct injection of DNA,
CaPO.sub.4 precipitation, gene gun techniques, electroporation,
liposomes, lipofection, and the like. Any of these methods are
widely available to one skilled in the art and would be suitable
for use in the present invention. Other suitable methods are
available to one skilled in the art, and it is to be understood
that the present invention can be accomplished using any of the
available methods of transfection. Lipofection can be accomplished
by encapsulating an isolated DNA molecule within a liposomal
particle and contacting the liposomal particle with the cell
membrane of the target cell. Liposomes are self-assembling,
colloidal particles in which a lipid bilayer, composed of
amphiphilic molecules such as phosphatidyl serine or phosphatidyl
choline, encapsulates a portion of the surrounding media such that
the lipid bilayer surrounds a hydrophilic interior. Unilammellar or
multilammellar liposomes can be constructed such that the interior
contains a desired chemical, drug, or, as in the instant invention,
an isolated DNA molecule.
Antibody Compositions, Fragments Thereof, and Other Binding
Agents
[0253] According to another aspect, the present invention further
provides compounds (e.g., small molecules) and other binding
agents, such as antibodies, antigen-binding fragments thereof,
soluble receptors, etc., that exhibit binding specificity for a
polypeptide or its binding partner disclosed herein, or to a
portion, variant or derivative thereof, and methods of using same.
Preferably, such binding agents are effective for modulating one or
more of the non-canonical activities mediated by a monomeric AARS
polypeptide of the invention. In certain embodiments, for example,
the binding agent is one that binds to a monomeric AARS polypeptide
of the invention and inhibits its ability to bind to one or more of
its cellular binding partners. In certain embodiments, the binding
agent does not substantially bind to an AARS dimer. A specific
example is a compound or binding agent that inhibits the ability of
HIV Gag to interact with monomeric KRS. Accordingly, such binding
agents may be used to treat or prevent diseases, disorders or other
conditions that are mediated by a monomeric AARS polypeptide of the
invention by antagonizing it activity.
[0254] In specific embodiments, compounds or binding agents (e.g.,
antibodies and fragments thereof) specifically bind to (a) an H3
and/or H4 region of a human immunodeficiency virus (HIV) Gag-CA-CTD
domain, (b) an inter-domain cavity of substantially monomeric KRS
which interacts with the H3 and/or H3 region of Gag-CA-CTD domain,
or both (a) and (b), and reduce the interaction between HIV Gag and
monomeric KRS. In certain embodiments, the compound or binding
agent binds to the bottom side of H3 or H4 or both. In certain
embodiments, the compound or binding agent mimics the
three-dimensional structure of the Gag-CA-CTD domain comprising the
H3 and/or H4 region. Also included are methods of reducing assembly
of a human immunodeficiency virus (HIV), comprising contacting an
HIV-infected cell with a compound or binding described above. Such
methods, compounds, and agents can be used in the treatment of HIV
infection.
[0255] An antibody, or antigen-binding fragment thereof, is said to
"specifically bind," "immunologically bind," and/or is
"immunologically reactive" to a polypeptide of the invention if it
reacts at a detectable level (within, for example, an ELISA assay)
with the polypeptide, and does not react detectably with unrelated
polypeptides under similar conditions.
[0256] Immunological binding, as used in this context, generally
refers to the non-covalent interactions of the type which occur
between an immunoglobulin molecule and an antigen for which the
immunoglobulin is specific. The strength, or affinity of
immunological binding interactions can be expressed in terms of the
dissociation constant (K.sub.d) of the interaction, wherein a
smaller K.sub.d represents a greater affinity. Immunological
binding properties of selected polypeptides can be quantified using
methods well known in the art. One such method entails measuring
the rates of antigen-binding site/antigen complex formation and
dissociation, wherein those rates depend on the concentrations of
the complex partners, the affinity of the interaction, and on
geometric parameters that equally influence the rate in both
directions. Thus, both the "on rate constant" (K.sub.on) and the
"off rate constant" (K.sub.off) can be determined by calculation of
the concentrations and the actual rates of association and
dissociation. The ratio of K.sub.off/K.sub.on enables cancellation
of all parameters not related to affinity, and is thus equal to the
dissociation constant K.sub.d. See, generally, Davies et al. (1990)
Annual Rev. Biochem. 59:439-473.
[0257] An "antigen-binding site," or "binding portion" of an
antibody, refers to the part of the immunoglobulin molecule that
participates in antigen binding. The antigen binding site is formed
by amino acid residues of the N-terminal variable ("V") regions of
the heavy ("H") and light ("L") chains. Three highly divergent
stretches within the V regions of the heavy and light chains are
referred to as "hypervariable regions" which are interposed between
more conserved flanking stretches known as "framework regions," or
"FRs". Thus the term "FR" refers to amino acid sequences which are
naturally found between and adjacent to hypervariable regions in
immunoglobulins. In an antibody molecule, the three hypervariable
regions of a light chain and the three hypervariable regions of a
heavy chain are disposed relative to each other in three
dimensional space to form an antigen-binding surface. The
antigen-binding surface is complementary to the three-dimensional
surface of a bound antigen, and the three hypervariable regions of
each of the heavy and light chains are referred to as
"complementarity-determining regions," or "CDRs."
[0258] A binding agent may be, for example, a ribosome, with or
without a peptide component, an RNA molecule or a polypeptide. In a
preferred embodiment, a binding agent is an antibody or an
antigen-binding fragment thereof. Antibodies may be prepared by any
of a variety of techniques known to those of ordinary skill in the
art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual,
Cold Spring Harbor Laboratory, 1988. In general, antibodies can be
produced by cell culture techniques, including the generation of
monoclonal antibodies as described herein, or via transfection of
antibody genes into suitable bacterial or mammalian cell hosts, in
order to allow for the production of recombinant antibodies. In one
technique, an immunogen comprising the polypeptide is initially
injected into any of a wide variety of mammals (e.g., mice, rats,
rabbits, sheep or goats). In this step, the polypeptides of this
invention may serve as the immunogen without modification.
Alternatively, particularly for relatively short polypeptides, a
superior immune response may be elicited if the polypeptide is
joined to a carrier protein, such as bovine serum albumin or
keyhole limpet hemocyanin. The immunogen is injected into the
animal host, preferably according to a predetermined schedule
incorporating one or more booster immunizations, and the animals
are bled periodically. Polyclonal antibodies specific for the
polypeptide may then be purified from such antisera by, for
example, affinity chromatography using the polypeptide coupled to a
suitable solid support.
[0259] Monoclonal antibodies specific for a polypeptide of interest
may be prepared, for example, using the technique of Kohler and
Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements
thereto. Briefly, these methods involve the preparation of immortal
cell lines capable of producing antibodies having the desired
specificity (i.e., reactivity with the polypeptide of interest).
Such cell lines may be produced, for example, from spleen cells
obtained from an animal immunized as described above. The spleen
cells are then immortalized by, for example, fusion with a myeloma
cell fusion partner, preferably one that is syngeneic with the
immunized animal. A variety of fusion techniques may be employed.
For example, the spleen cells and myeloma cells may be combined
with a nonionic detergent for a few minutes and then plated at low
density on a selective medium that supports the growth of hybrid
cells, but not myeloma cells. A preferred selection technique uses
HAT (hypoxanthine, aminopterin, thymidine) selection. After a
sufficient time, usually about 1 to 2 weeks, colonies of hybrids
are observed. Single colonies are selected and their culture
supernatants tested for binding activity against the polypeptide.
Hybridomas having high reactivity and specificity are
preferred.
[0260] Monoclonal antibodies may be isolated from the supernatants
of growing hybridoma colonies. In addition, various techniques may
be employed to enhance the yield, such as injection of the
hybridoma cell line into the peritoneal cavity of a suitable
vertebrate host, such as a mouse. Monoclonal antibodies may then be
harvested from the ascites fluid or the blood. Contaminants may be
removed from the antibodies by conventional techniques, such as
chromatography, gel filtration, precipitation, and extraction. The
polypeptides of this invention may be used in the purification
process in, for example, an affinity chromatography step.
[0261] A number of therapeutically useful molecules are known in
the art which comprise antigen-binding sites that are capable of
exhibiting immunological binding properties of an antibody
molecule. The proteolytic enzyme papain preferentially cleaves IgG
molecules to yield several fragments, two of which (the "F(ab)"
fragments) each comprise a covalent heterodimer that includes an
intact antigen-binding site. The enzyme pepsin is able to cleave
IgG molecules to provide several fragments, including the
"F(ab').sub.2" fragment which comprises both antigen-binding sites.
An "Fv" fragment can be produced by preferential proteolytic
cleavage of an IgM, and on rare occasions IgG or IgA immunoglobulin
molecule. Fv fragments are, however, more commonly derived using
recombinant techniques known in the art. The Fv fragment includes a
non-covalent V.sub.H::V.sub.L heterodimer including an
antigen-binding site which retains much of the antigen recognition
and binding capabilities of the native antibody molecule. Inbar et
al. (1972) Proc. Nat. Acad. Sci. USA 69:2659-2662; Hochman et al.
(1976) Biochem 15:2706-2710; and Ehrlich et al. (1980) Biochem
19:4091-4096.
[0262] A single chain Fv ("sFv") polypeptide is a covalently linked
V.sub.H::V.sub.L heterodimer which is expressed from a gene fusion
including V.sub.H- and V.sub.L-encoding genes linked by a
peptide-encoding linker. Huston et al. (1988) Proc. Nat. Acad. Sci.
USA 85(16):5879-5883. A number of methods have been described to
discern chemical structures for converting the naturally
aggregated--but chemically separated--light and heavy polypeptide
chains from an antibody V region into an sFv molecule which will
fold into a three dimensional structure substantially similar to
the structure of an antigen-binding site. See, e.g., U.S. Pat. Nos.
5,091,513 and 5,132,405, to Huston et al.; and U.S. Pat. No.
4,946,778, to Ladner et al.
[0263] Each of the above-described molecules includes a heavy chain
and a light chain CDR set, respectively interposed between a heavy
chain and a light chain FR set which provide support to the CDRS
and define the spatial relationship of the CDRs relative to each
other. As used herein, the term "CDR set" refers to the three
hypervariable regions of a heavy or light chain V region.
Proceeding from the N-terminus of a heavy or light chain, these
regions are denoted as "CDR1," "CDR2," and "CDR3" respectively. An
antigen-binding site, therefore, includes six CDRs, comprising the
CDR set from each of a heavy and a light chain V region. A
polypeptide comprising a single CDR, (e.g., a CDR1, CDR2 or CDR3)
is referred to herein as a "molecular recognition unit."
Crystallographic analysis of a number of antigen-antibody complexes
has demonstrated that the amino acid residues of CDRs form
extensive contact with bound antigen, wherein the most extensive
antigen contact is with the heavy chain CDR3. Thus, the molecular
recognition units are primarily responsible for the specificity of
an antigen-binding site.
[0264] As used herein, the term "FR set" refers to the four
flanking amino acid sequences which frame the CDRs of a CDR set of
a heavy or light chain V region. Some FR residues may contact bound
antigen; however, FRs are primarily responsible for folding the V
region into the antigen-binding site, particularly the FR residues
directly adjacent to the CDRS. Within FRs, certain amino residues
and certain structural features are very highly conserved. In this
regard, all V region sequences contain an internal disulfide loop
of around 90 amino acid residues. When the V regions fold into a
binding-site, the CDRs are displayed as projecting loop motifs
which form an antigen-binding surface. It is generally recognized
that there are conserved structural regions of FRs which influence
the folded shape of the CDR loops into certain "canonical"
structures--regardless of the precise CDR amino acid sequence.
Further, certain FR residues are known to participate in
non-covalent interdomain contacts which stabilize the interaction
of the antibody heavy and light chains.
[0265] A number of "humanized" antibody molecules comprising an
antigen-binding site derived from a non-human immunoglobulin have
been described, including chimeric antibodies having rodent V
regions and their associated CDRs fused to human constant domains
(Winter et al. (1991) Nature 349:293-299; Lobuglio et al. (1989)
Proc. Nat. Acad. Sci. USA 86:4220-4224; Shaw et al. (1987) J
Immunol. 138:4534-4538; and Brown et al. (1987) Cancer Res.
47:3577-3583), rodent CDRs grafted into a human supporting FR prior
to fusion with an appropriate human antibody constant domain
(Riechmann et al. (1988) Nature 332:323-327; Verhoeyen et al.
(1988) Science 239:1534-1536; and Jones et al. (1986) Nature
321:522-525), and rodent CDRs supported by recombinantly veneered
rodent FRs (European Patent Publication No. 519,596, published Dec.
23, 1992). These "humanized" molecules are designed to minimize
unwanted immunological response toward rodent antihuman antibody
molecules which limits the duration and effectiveness of
therapeutic applications of those moieties in human recipients.
[0266] As used herein, the terms "veneered FRs" and "recombinantly
veneered FRs" refer to the selective replacement of FR residues
from, e.g., a rodent heavy or light chain V region, with human FR
residues in order to provide a xenogeneic molecule comprising an
antigen-binding site which retains substantially all of the native
FR polypeptide folding structure. Veneering techniques are based on
the understanding that the ligand binding characteristics of an
antigen-binding site are determined primarily by the structure and
relative disposition of the heavy and light chain CDR sets within
the antigen-binding surface. Davies et al. (1990) Ann. Rev.
Biochem. 59:439-473. Thus, antigen binding specificity can be
preserved in a humanized antibody only wherein the CDR structures,
their interaction with each other, and their interaction with the
rest of the V region domains are carefully maintained. By using
veneering techniques, exterior (e.g., solvent-accessible) FR
residues which are readily encountered by the immune system are
selectively replaced with human residues to provide a hybrid
molecule that comprises either a weakly immunogenic, or
substantially non-immunogenic veneered surface.
[0267] In another embodiment of the invention, monoclonal
antibodies of the present invention may be coupled to one or more
agents of interest. For example, a therapeutic agent may be coupled
(e.g., covalently bonded) to a suitable monoclonal antibody either
directly or indirectly (e.g., via a linker group). A direct
reaction between an agent and an antibody is possible when each
possesses a substituent capable of reacting with the other. For
example, a nucleophilic group, such as an amino or sulfhydryl
group, on one may be capable of reacting with a carbonyl-containing
group, such as an anhydride or an acid halide, or with an alkyl
group containing a good leaving group (e.g., a halide) on the
other.
[0268] Alternatively, it may be desirable to couple a therapeutic
agent and an antibody via a linker group. A linker group can
function as a spacer to distance an antibody from an agent in order
to avoid interference with binding capabilities. A linker group can
also serve to increase the chemical reactivity of a substituent on
an agent or an antibody, and thus increase the coupling efficiency.
An increase in chemical reactivity may also facilitate the use of
agents, or functional groups on agents, which otherwise would not
be possible.
[0269] It will be evident to those skilled in the art that a
variety of bifunctional or polyfunctional reagents, both homo- and
hetero-functional (such as those described in the catalog of the
Pierce Chemical Co., Rockford, Ill.), may be employed as the linker
group. Coupling may be effected, for example, through amino groups,
carboxyl groups, sulfhydryl groups or oxidized carbohydrate
residues. There are numerous references describing such
methodology, e.g., U.S. Pat. No. 4,671,958, to Rodwell et al.
[0270] Where a therapeutic agent is more potent when free from the
antibody portion of the immunoconjugates of the present invention,
it may be desirable to use a linker group which is cleavable during
or upon internalization into a cell. A number of different
cleavable linker groups have been described. The mechanisms for the
intracellular release of an agent from these linker groups include
cleavage by reduction of a disulfide bond (e.g., U.S. Pat. No.
4,489,710, to Spitler), by irradiation of a photolabile bond (e.g.,
U.S. Pat. No. 4,625,014, to Senter et al.), by hydrolysis of
derivatized amino acid side chains (e.g., U.S. Pat. No. 4,638,045,
to Kohn et al.), by serum complement-mediated hydrolysis (e.g.,
U.S. Pat. No. 4,671,958, to Rodwell et al.), and acid-catalyzed
hydrolysis (e.g., U.S. Pat. No. 4,569,789, to Blattler et al.).
[0271] It may be desirable to couple more than one agent to an
antibody. In one embodiment, multiple molecules of an agent are
coupled to one antibody molecule. In another embodiment, more than
one type of agent may be coupled to one antibody. Regardless of the
particular embodiment, immunoconjugates with more than one agent
may be prepared in a variety of ways. For example, more than one
agent may be coupled directly to an antibody molecule, or linkers
that provide multiple sites for attachment can be used.
Methods of Screening
[0272] Certain embodiments relate to the use of monomeric AARS
polypeptides, antibodies, or polynucleotide references sequences in
drug discovery, typically to identify agents that modulate one or
more of the non-canonical activities of a monomeric AARS
polypeptide. For example, certain embodiments include methods of
identifying one or more "binding partners" of an AARS monomeric
polypeptide, such as a cellular proteins, viral proteins, bacterial
proteins, etc., that directly or physically interact with the AARS
polypeptide.
[0273] Also included are methods of identifying host molecules that
participate in one or more non-canonical activities of the
monomeric AARS polypeptide, including molecules that directly or
indirectly interact with the cellular binding partner, and either
regulate its role in a non-canonical activity, or are regulated by
the binding partner. Such host molecules include both upstream and
downstream components of the non-canonical pathway, typically
related by about 1, 2, 3, 4, 5 or more identifiable steps in the
pathway, relative to the binding partner/monomeric AARS protein
interaction.
[0274] Certain aspects include methods of identifying a compound
(e.g., polypeptide) or other agent that agonizes or antagonizes the
non-canonical activity of a monomeric AARS polypeptide or active
variant thereof, such as by interacting with the monomeric AARS
polypeptide and/or one or more of its binding partners. Also
included are methods of identifying agents that modulate the
expression (e.g., splicing) of AARS splice variants, or modulate
the activity of proteases that otherwise regulate the production of
endogenous AARS protein fragments (resectins) at the protein
level.
[0275] Certain embodiments therefore include methods of identifying
a binding partner of an monomeric AARS polypeptide, comprising a)
combining the monomeric AARS polypeptide with a biological sample
under suitable conditions, and b) detecting specific binding of the
monomeric AARS polypeptide to a binding partner, thereby
identifying a binding partner that specifically binds to the AARS
polypeptide. Also included are methods of screening for a compound
that specifically binds to a monomeric AARS polypeptide or a
binding partner of the AARS polypeptide, comprising a) combining
the polypeptide or the binding partner with at least one test
compound under suitable conditions, and b) detecting binding of the
polypeptide or the binding partner to the test compound, thereby
identifying a compound that specifically binds to the polypeptide
or its binding partner. In certain embodiments, the compound is a
polypeptide or peptide. In certain embodiments, the compound is a
small molecule or other (e.g., non-biological) chemical compound.
In certain embodiments, the compound is a peptide mimetic.
[0276] Any method suitable for detecting protein-protein
interactions may be employed for identifying cellular proteins that
interact with an AARS reference polypeptide, interact with one or
more of its binding partner(s), or both. Examples of traditional
methods that may be employed include co-immunoprecipitation,
cross-linking, and co-purification through gradients or
chromatographic columns of cell lysates or proteins obtained from
cell lysates, mainly to identify proteins in the lysate that
interact with the monomeric AARS polypeptide.
[0277] In these and related embodiments, at least a portion of the
amino acid sequence of a protein that interacts with a monomeric
AARS polypeptide or its binding partner can be ascertained using
techniques well known to those of skill in the art, such as via the
Edman degradation technique. See, e.g., Creighton Proteins:
Structures and Molecular Principles, W. H. Freeman & Co., N.Y.,
pp. 34 49, 1983. The amino acid sequence obtained may be used as a
guide for the generation of oligonucleotide mixtures that can be
used to screen for gene sequences encoding such proteins. Screening
may be accomplished, for example, by standard hybridization or PCR
techniques, as described herein and known in the art. Techniques
for the generation of oligonucleotide mixtures and the screening
are well known. See, e.g., Ausubel et al. Current Protocols in
Molecular Biology Green Publishing Associates and Wiley
Interscience, N.Y., 1989; and Innis et al., eds. PCR Protocols: A
Guide to Methods and Applications Academic Press, Inc., New York,
1990.
[0278] Additionally, methods may be employed in the simultaneous
identification of genes that encode the binding partner or other
polypeptide. These methods include, for example, probing expression
libraries, in a manner similar to the well known technique of
antibody probing of lambda-gt11 libraries, using labeled monomeric
AARS protein, or another polypeptide, peptide or fusion protein,
e.g., a variant AARS polypeptide or AARS domain fused to a marker
(e.g., an enzyme, fluor, luminescent protein, or dye), or an Ig-Fc
domain.
[0279] One method that detects protein interactions in vivo, the
two-hybrid system, is described in detail for illustration only and
not by way of limitation. One example of this system has been
described (Chien et al., PNAS USA 88:9578 9582, 1991) and is
commercially available from Clontech (Palo Alto, Calif.).
[0280] Briefly, utilizing such a system, plasmids may be
constructed that encode two hybrid proteins: one plasmid consists
of nucleotides encoding the DNA-binding domain of a transcription
activator protein fused to a monomeric AARS reference nucleotide
sequence (or, in certain embodiments, its binding partner), or a
variant thereof, and the other plasmid consists of nucleotides
encoding the transcription activator protein's activation domain
fused to a cDNA (or collection of cDNAs) encoding an unknown
protein(s) that has been recombined into the plasmid as part of a
cDNA library. The DNA-binding domain fusion plasmid and the
activator cDNA library may be transformed into a strain of the
yeast Saccharomyces cerevisiae that contains a reporter gene (e.g.,
HBS or lacZ) whose regulatory region contains the transcription
activator's binding site. Either hybrid protein alone cannot
activate transcription of the reporter gene: the DNA-binding domain
hybrid cannot because it does not provide activation function and
the activation domain hybrid cannot because it cannot localize to
the activator's binding sites. Interaction of the two hybrid
proteins reconstitutes the functional activator protein and results
in expression of the reporter gene, which is detected by an assay
for the reporter gene product.
[0281] The two-hybrid system or other such methodology may be used
to screen activation domain libraries for proteins that interact
with the "bait" gene product. By way of example, and not by way of
limitation, an AARS reference polypeptide or variant may be used as
the bait gene product. A monomeric AARS binding partner may also be
used as a "bait" gene product. Total genomic or cDNA sequences are
fused to the DNA encoding an activation domain. This library and a
plasmid encoding a hybrid of a bait AARS gene product fused to the
DNA-binding domain are co-transformed into a yeast reporter strain,
and the resulting transformants are screened for those that express
the reporter gene.
[0282] A cDNA library of the cell line from which proteins that
interact with bait AARS gene products are to be detected can be
made using methods routinely practiced in the art. For example, the
cDNA fragments can be inserted into a vector such that they are
translationally fused to the transcriptional activation domain of
GAL4. This library can be co-transformed along with the bait
gene-GAL4 fusion plasmid into a yeast strain, which contains a lacZ
gene driven by a promoter that contains GAL4 activation sequence. A
cDNA encoded protein, fused to GAL4 transcriptional activation
domain, that interacts with bait gene product will reconstitute an
active GAL4 protein and thereby drive expression of the HIS3 gene.
Colonies, which express HIS3, can be detected by their growth on
Petri dishes containing semi-solid agar based media lacking
histidine. The cDNA can then be purified from these strains, and
used to produce and isolate the bait AARS gene-interacting protein
using techniques routinely practiced in the art.
[0283] Also included are three-hybrid systems, which allow the
detection of RNA-protein interactions in yeast. See, e.g., Hook et
al., RNA. 11:227-233, 2005. Accordingly, these and related methods
can be used to identify a binding partner of a monomeric AARS
polypeptide, and to identify other proteins or nucleic acids that
interact with the AARS polypeptide, its binding partner, or both.
These and related methods can also be used to identify compounds
that interfere with the interaction between a monomeric AARS
polypeptide and one or more of its binding partners (e.g., cellular
proteins, viral proteins, bacterial proteins).
[0284] Certain embodiments relate to the use of interactome
screening approaches. Particular examples include protein
domain-based screening (see, e.g., Boxem et al., Cell. 134:534-545,
2008; and Yu et al., Science. 322:10-110, 2008).
[0285] As noted above, once isolated, binding partners can be
identified and can, in turn, be used in conjunction with standard
techniques to identify proteins or other compounds with which it
interacts. Certain embodiments thus relate to methods of screening
for a compound that specifically binds to the binding partner of a
monomeric AARS polypeptide, comprising a) combining the binding
partner with at least one test compound under suitable conditions,
and b) detecting binding of the binding partner to the test
compound, thereby identifying a compound that specifically binds to
the binding partner. In certain embodiments, the test compound is a
polypeptide. In certain embodiments, the test compound is a
chemical compound, such as a small molecule compound or peptide
mimetic. In specific embodiments, the binding partner is an HIV Gag
protein and the AARS polypeptide is a monomeric form of KRS.
[0286] Certain embodiments include methods of screening for a
compound that modulates the activity of a monomeric AARS
polypeptide, comprising a) combining the polypeptide with at least
one test compound under conditions permissive for the activity of
the polypeptide, b) assessing the activity of the polypeptide in
the presence of the test compound, and c) comparing the activity of
the polypeptide in the presence of the test compound with the
activity of the polypeptide in the absence of the test compound,
wherein a change in the activity of the polypeptide in the presence
of the test compound is indicative of a compound that modulates the
activity of the polypeptide.
[0287] Certain embodiments include methods of screening for a
compound that modulates the activity of a binding partner of a
monomeric AARS polypeptide, comprising a) combining the polypeptide
with at least one test compound under conditions permissive for the
activity of the binding partner, b) assessing the activity of the
binding partner in the presence of the test compound, and c)
comparing the activity of the binding partner in the presence of
the test compound with the activity of the binding partner in the
absence of the test compound, wherein a change in the activity of
the binding partner in the presence of the test compound is
indicative of a compound that modulates the activity of the binding
partner. Typically, these and related embodiments include assessing
a selected non-canonical activity that is associated with the AARS
polypeptide or its binding partner. Included are in vitro and in
vivo conditions, such as cell culture conditions.
[0288] Certain embodiments include methods of screening a compound
for effectiveness as a full or partial agonist of a monomeric AARS
reference polypeptide or an active fragment or variant thereof,
comprising a) exposing a sample comprising the polypeptide to a
compound, and b) detecting agonist activity in the sample,
typically by measuring an increase in the non-canonical activity of
the monomeric AARS polypeptide. Certain methods include a) exposing
a sample comprising a binding partner of the AARS polypeptide to a
compound, and b) detecting agonist activity in the sample,
typically by measuring an increase in the selected non-canonical
activity of the AARS polypeptide. Certain embodiments include
compositions that comprise an agonist compound identified by the
method and a pharmaceutically acceptable carrier or excipient.
[0289] Also included are methods of screening a compound for
effectiveness as a full or partial antagonist of a monomeric AARS
polypeptide, comprising a) exposing a sample comprising the
polypeptide to a compound, and b) detecting antagonist activity in
the sample, typically by measuring a decrease in the non-canonical
activity of the AARS polypeptide. Certain methods include a)
exposing a sample comprising a binding partner of the AARS
polypeptide to a compound, and b) detecting antagonist activity in
the sample, typically by measuring a decrease in the selected
non-canonical activity of the AARS polypeptide. Certain embodiments
include compositions that comprise an antagonist compound
identified by the method and a pharmaceutically acceptable carrier
or excipient.
[0290] Specific embodiments include, for example, compositions that
can be used for drug discovery or treatment (e.g., in vitro
compositions), comprising a human immunodeficiency virus (HIV) Gag
protein and a substantially monomeric lysyl tRNA synthetase (KRS)
described herein, which typically or optionally comprises one or
more stabilizing modifications that do not significantly reduce KRS
binding to HIV Gag. Also included are modified cells, comprising a
human immunodeficiency virus (HIV) Gag protein and an exogenous
(e.g., recombinantly introduced), substantially monomeric lysyl
tRNA synthetase (KRS) polypeptide described herein, which comprises
one or more stabilizing modifications that do not significantly
reduce KRS binding to HIV Gag. In some embodiments, the HIV Gag
protein comprises the Gag-CA-CTD domain. In specific embodiments,
the Gag-CA-CTD domain comprises regions H3 and H4.
[0291] Other specific embodiments include methods of identifying a
compound that specifically reduces binding between a human
immunodeficiency virus (HIV) Gag protein and a substantially
monomeric lysyl tRNA synthetase (KRS) polypeptide, comprising (a)
combining the composition or cell described above with at least one
test compound under suitable conditions, and (b) detecting reduced
binding between the HIV Gag protein and the substantially monomer
KRS polypeptide, thereby identifying a compound that specifically
reduces binding between the HIV Gag protein and the KRS
polypeptide. In certain embodiments, the test compound is a
polypeptide or peptide, an antibody or antigen-binding fragment
thereof, a peptide mimetic, or a small molecule. In some
embodiments, the test compound binds to the Gag-CA-CTD domain. In
particular embodiments, the test compound binds to H3 or H4 or both
of the Gag-CA-CTD domain. In specific embodiments, the test
compound binds to the bottom side of H3 or H4 or both (see FIG.
18E).
[0292] In certain embodiments, in vitro systems may be designed to
identify compounds capable of interacting with or modulating an
AARS reference sequence or its binding partner. Certain of the
compounds identified by such systems may be useful, for example, in
modulating the activity of the pathway, and in elaborating
components of the pathway itself. They may also be used in screens
for identifying compounds that disrupt interactions between
components of the pathway; or may disrupt such interactions
directly. One exemplary approach involves preparing a reaction
mixture of the AARS polypeptide and a test compound under
conditions and for a time sufficient to allow the two to interact
and bind, thus forming a complex that can be removed from and/or
detected in the reaction mixture
[0293] In vitro screening assays can be conducted in a variety of
ways. For example, a monomeric AARS polypeptide, a binding partner,
and/or test compound(s) can be anchored onto a solid phase. In
these and related embodiments, the resulting complexes may be
captured and detected on the solid phase at the end of the
reaction. In one example of such a method, the monomeric AARS
polypeptide and/or its binding partner are anchored onto a solid
surface, and the test compound(s), which are not anchored, may be
labeled, either directly or indirectly, so that their capture by
the component on the solid surface can be detected. In other
examples, the test compound(s) are anchored to the solid surface,
and the AARS polypeptide and/or its binding partner, which are not
anchored, are labeled or in some way detectable. In certain
embodiments, microtiter plates may conveniently be utilized as the
solid phase. The anchored component (or test compound) may be
immobilized by non-covalent or covalent attachments. Non-covalent
attachment may be accomplished by simply coating the solid surface
with a solution of the protein and drying. Alternatively, an
immobilized antibody, preferably a monoclonal antibody, specific
for the protein to be immobilized may be used to anchor the protein
to the solid surface. The surfaces may be prepared in advance and
stored.
[0294] To conduct an exemplary assay, the non-immobilized component
is typically added to the coated surface containing the anchored
component. After the reaction is complete, un-reacted components
are removed (e.g., by washing) under conditions such that any
specific complexes formed will remain immobilized on the solid
surface. The detection of complexes anchored on the solid surface
can be accomplished in a number of ways. For instance, where the
previously non-immobilized component is pre-labeled, the detection
of label immobilized on the surface indicates that complexes were
formed. Where the previously non-immobilized component is not
pre-labeled, an indirect label can be used to detect complexes
anchored on the surface; e.g., using a labeled antibody specific
for the previously non-immobilized component (the antibody, in
turn, may be directly labeled or indirectly labeled with a labeled
anti-Ig antibody).
[0295] Alternatively, the presence or absence of binding of a test
compound can be determined, for example, using surface plasmon
resonance (SPR) and the change in the resonance angle as an index,
wherein an AARS polypeptide or a cellular binding partner is
immobilized onto the surface of a commercially available sensorchip
(e.g., manufactured by Biacore.TM.) according to a conventional
method, the test compound is contacted therewith, and the
sensorchip is illuminated with a light of a particular wavelength
from a particular angle. The binding of a test compound can also be
measured by detecting the appearance of a peak corresponding to the
test compound by a method wherein an AARS polypeptide or a cellular
binding partner is immobilized onto the surface of a protein chip
adaptable to a mass spectrometer, a test compound is contacted
therewith, and an ionization method such as MALDI-MS, ESI-MS,
FAB-MS and the like is combined with a mass spectrometer (e.g.,
double-focusing mass spectrometer, quadrupole mass spectrometer,
time-of-flight mass spectrometer, Fourier transformation mass
spectrometer, ion cyclotron mass spectrometer and the like).
[0296] In certain embodiments, cell-based assays, membrane
vesicle-based assays, or membrane fraction-based assays can be used
to identify compounds that modulate interactions in the
non-canonical pathway of the selected AARS polypeptide. To this
end, cell lines that express an AARS polypeptide and/or a binding
partner, or a fusion protein containing a domain or fragment of
such proteins (or a combination thereof), or cell lines (e.g., COS
cells, CHO cells, HEK293 cells, Hela cells etc.) that have been
genetically engineered to express such protein(s) or fusion
protein(s) can be used. Test compound(s) that influence the
non-canonical activity can be identified by monitoring a change
(e.g., a statistically significant change) in that activity as
compared to a control or a predetermined amount.
[0297] Antibodies to AARS monomers can also be used in screening
assays, such as to identify an agent that specifically binds to an
AARS, confirm the specificity or affinity of an agent that binds to
an AARS monomer, or identify the site of interaction between the
agent and the AARS monomer. Included are assays in which the
antibody is used as a competitive inhibitor of the agent. For
instance, an antibody that specifically binds to an AARS monomer
with a known affinity can act as a competitive inhibitor of a
selected agent, and be used to calculate the affinity of the agent
for the AARS monomer. Also, one or more antibodies that
specifically bind to known epitopes or sites of an AARS monomer can
be used as a competitive inhibitor to confirm whether or not the
agent binds at that same site. Other variations will be apparent to
persons skilled in the art.
[0298] Also included are any of the above methods, or other
screening methods known in the art, which are adapted for
high-throughput screening (HTS). HTS typically uses automation to
run a screen of an assay against a library of candidate compounds,
for instance, an assay that measures an increase or a decrease in a
non-canonical activity, as described herein.
[0299] Any of the screening methods provided herein may utilize
small molecule libraries or libraries generated by combinatorial
chemistry. Libraries of chemical and/or biological mixtures, such
as fungal, bacterial, or algal extracts, are known in the art and
can be screened with any of the assays of the invention. Examples
of methods for the synthesis of molecular libraries can be found
in: (Carell et al., 1994a; Carell et al., 1994b; Cho et al., 1993;
DeWitt et al., 1993; Gallop et al., 1994; Zuckermann et al.,
1994).
[0300] Libraries of compounds may be presented in solution
(Houghten et al., 1992) or on beads (Lam et al., 1991), on chips
(Fodor et al., 1993), bacteria, spores (Ladner et al., U.S. Pat.
No. 5,223,409, 1993), plasmids (Cull et al., 1992) or on phage
(Cwirla et al., 1990; Devlin et al., 1990; Felici et al., 1991;
Ladner et al., U.S. Pat. No. 5,223,409, 1993; Scott and Smith,
1990). Embodiments of the present invention encompass the use of
different libraries for the identification of small molecule
modulators of one or more AARS monomers, their binding partners,
and/or their related non-canonical activities. Libraries useful for
the purposes of the invention include, but are not limited to, (1)
chemical libraries, (2) natural product libraries, and (3)
combinatorial libraries comprised of random peptides,
oligonucleotides and/or organic molecules.
[0301] Chemical libraries consist of structural analogs of known
compounds or compounds that are identified as "hits" or "leads" via
natural product screening. Natural product libraries are derived
from collections of microorganisms, animals, plants, or marine
organisms which are used to create mixtures for screening by: (1)
fermentation and extraction of broths from soil, plant or marine
microorganisms or (2) extraction of plants or marine organisms.
Natural product libraries include polyketides, non-ribosomal
peptides, and variants (non-naturally occurring) thereof. See,
e.g., Cane et al., Science 282:63-68, 1998. Combinatorial libraries
may be composed of large numbers of peptides, oligonucleotides or
organic compounds as a mixture. They are relatively easy to prepare
by traditional automated synthesis methods, PCR, cloning or
proprietary synthetic methods.
[0302] More specifically, a combinatorial chemical library is a
collection of diverse chemical compounds generated by either
chemical synthesis or biological synthesis, by combining a number
of chemical "building blocks" such as reagents. For example, a
linear combinatorial chemical library such as a polypeptide library
is formed by combining a set of chemical building blocks (amino
acids) in every possible way for a given compound length (i.e., the
number of amino acids in a polypeptide compound). Millions of
chemical compounds can be synthesized through such combinatorial
mixing of chemical building blocks.
[0303] For a review of combinatorial chemistry and libraries
created therefrom, see, e.g., Huc, I. and Nguyen, R. (2001) Comb.
Chem. High Throughput Screen 4:53-74; Lepre, C A. (2001) Drug
Discov. Today 6:133-140; Peng, S. X. (2000) Biomed. Chromatogr.
14:430-441; Bohm, H. J. and Stahl, M. (2000) Curr. Opin. Chem.
Biol. 4:283-286; Barnes, C and Balasubramanian, S. (2000) Curr.
Opin. Chem. Biol. 4:346-350; Lepre, Enjalbal, C, et al., (2000)
Mass Septrom Rev. 19:139-161; Hall, D. G., (2000) Nat. Biotechnol.
18:262-262; Lazo, J. S., and Wipf, P. (2000) J. Pharmacol. Exp.
Ther. 293:705-709; Houghten, R. A., (2000) Ann. Rev. Pharmacol.
Toxicol. 40:273-282; Kobayashi, S. (2000) Curr. Opin. Chem. Biol.
(2000) 4:338-345; Kopylov, A. M. and Spiridonova, V. A. (2000) Mol.
Biol. (Mosk) 34:1097-1113; Weber, L. (2000) Curr. Opin. Chem. Biol.
4:295-302; Dolle, R. E. (2000) J. Comb. Chem. 2:383-433; Floyd, C
D., et al., (1999) Prog. Med. Chem. 36:91-168; Kundu, B., et al.,
(1999) Prog. Drug Res. 53:89-156; Cabilly, S. (1999) Mol.
Biotechnol. 12:143-148; Lowe, G. (1999) Nat. Prod. Rep. 16:641-651;
Dolle, R. E. and Nelson, K. H. (1999) J. Comb. Chem. 1:235-282;
Czarnick, A. W. and Keene, J. D. (1998) Curr. Biol. 8:R705-R707;
Dolle, R. E. (1998) Mol. Divers. 4:233-256; Myers, P. L., (1997)
Curr. Opin. Biotechnol. 8:701-707; and Pluckthun, A. and Cortese,
R. (1997) Biol. Chem. 378:443.
[0304] Devices for the preparation of combinatorial libraries are
commercially available (see, e.g., 357 MPS, 390 MPS, Advanced Chem
Tech, Louisville Ky., Symphony, Rainin, Woburn, Mass., 433A Applied
Biosystems, Foster City, Calif., 9050 Plus, Millipore, Bedford,
Mass.). In addition, numerous combinatorial libraries are
themselves commercially available (see, e.g., ComGenex, Princeton,
N.J., Asinex, Moscow, Ru, Tripos, Inc., St. Louis, Mo., ChemStar,
Ltd., Moscow, RU, 3D Pharmaceuticals, Exton, Pa., Martek
Biosciences, Columbia, Md., etc.).
Formulation and Administration
[0305] The compositions of the invention (e.g., polypeptides,
polynucleotides, antibodies, etc.) are generally formulated in
pharmaceutically-acceptable or physiologically-acceptable solutions
for administration to a cell, tissue or animal, either alone, or in
combination with one or more other modalities of therapy. It will
also be understood that, if desired, the compositions of the
invention may be administered in combination with other agents as
well, such as, e.g., other proteins or polypeptides or various
pharmaceutically-active agents. There is virtually no limit to
other components that may also be included in the compositions,
provided that the additional agents do not adversely affect the
desired effects desired to be achieved with an AARS polypeptide of
the invention.
[0306] In the pharmaceutical compositions of the invention,
formulation of pharmaceutically-acceptable excipients and carrier
solutions is well-known to those of skill in the art, as is the
development of suitable dosing and treatment regimens for using the
particular compositions described herein in a variety of treatment
regimens, including e.g., oral, parenteral, intravenous,
intranasal, intracranial and intramuscular administration and
formulation.
[0307] In certain applications, the pharmaceutical compositions
disclosed herein may be delivered via oral administration to a
subject. As such, these compositions may be formulated with an
inert diluent or with an assimilable edible carrier, or they may be
enclosed in hard- or soft-shell gelatin capsule, or they may be
compressed into tablets, or they may be incorporated directly with
the food of the diet.
[0308] In certain circumstances it will be desirable to deliver the
pharmaceutical compositions disclosed herein parenterally,
intravenously, intramuscularly, or even intraperitoneally as
described, for example, in U.S. Pat. No. 5,543,158; U.S. Pat. No.
5,641,515 and U.S. Pat. No. 5,399,363 (each specifically
incorporated herein by reference in its entirety). Solutions of the
active compounds as free base or pharmacologically acceptable salts
may be prepared in water suitably mixed with a surfactant, such as
hydroxypropylcellulose. Dispersions may also be prepared in
glycerol, liquid polyethylene glycols, and mixtures thereof and in
oils. Under ordinary conditions of storage and use, these
preparations contain a preservative to prevent the growth of
microorganisms.
[0309] The pharmaceutical forms suitable for injectable use include
sterile aqueous solutions or dispersions and sterile powders for
the extemporaneous preparation of sterile injectable solutions or
dispersions (U.S. Pat. No. 5,466,468, specifically incorporated
herein by reference in its entirety). In all cases the form should
be sterile and should be fluid to the extent that easy
syringability exists. It should be stable under the conditions of
manufacture and storage and should be preserved against the
contaminating action of microorganisms, such as bacteria and fungi.
The carrier can be a solvent or dispersion medium containing, for
example, water, ethanol, polyol (e.g., glycerol, propylene glycol,
and liquid polyethylene glycol, and the like), suitable mixtures
thereof, and/or vegetable oils. Proper fluidity may be maintained,
for example, by the use of a coating, such as lecithin, by the
maintenance of the required particle size in the case of dispersion
and by the use of surfactants. The prevention of the action of
microorganisms can be facilitated by various antibacterial and
antifungal agents, for example, parabens, chlorobutanol, phenol,
sorbic acid, thimerosal, and the like. In many cases, it will be
preferable to include isotonic agents, for example, sugars or
sodium chloride. Prolonged absorption of the injectable
compositions can be brought about by the use in the compositions of
agents delaying absorption, for example, aluminum monostearate and
gelatin.
[0310] For parenteral administration in an aqueous solution, for
example, the solution should be suitably buffered if necessary and
the liquid diluent first rendered isotonic with sufficient saline
or glucose. These particular aqueous solutions are especially
suitable for intravenous, intramuscular, subcutaneous and
intraperitoneal administration. In this connection, a sterile
aqueous medium that can be employed will be known to those of skill
in the art in light of the present disclosure. For example, one
dosage may be dissolved in 1 ml of isotonic NaCl solution and
either added to 1000 ml of hypodermoclysis fluid or injected at the
proposed site of infusion (see, e.g., Remington's Pharmaceutical
Sciences, 15th Edition, pp. 1035-1038 and 1570-1580). Some
variation in dosage will necessarily occur depending on the
condition of the subject being treated. The person responsible for
administration will, in any event, determine the appropriate dose
for the individual subject. Moreover, for human administration,
preparations should meet sterility, pyrogenicity, and the general
safety and purity standards as required by FDA Office of Biologics
standards.
[0311] Sterile injectable solutions can be prepared by
incorporating the active compounds in the required amount in the
appropriate solvent with the various other ingredients enumerated
above, as required, followed by filtered sterilization. Generally,
dispersions are prepared by incorporating the various sterilized
active ingredients into a sterile vehicle which contains the basic
dispersion medium and the required other ingredients from those
enumerated above. In the case of sterile powders for the
preparation of sterile injectable solutions, the preferred methods
of preparation are vacuum-drying and freeze-drying techniques which
yield a powder of the active ingredient plus any additional desired
ingredient from a previously sterile-filtered solution thereof.
[0312] The compositions disclosed herein may be formulated in a
neutral or salt form. Pharmaceutically-acceptable salts, include
the acid addition salts (formed with the free amino groups of the
protein) and which are formed with inorganic acids such as, for
example, hydrochloric or phosphoric acids, or such organic acids as
acetic, oxalic, tartaric, mandelic, and the like. Salts formed with
the free carboxyl groups can also be derived from inorganic bases
such as, for example, sodium, potassium, ammonium, calcium, or
ferric hydroxides, and such organic bases as isopropylamine,
trimethylamine, histidine, procaine and the like. Upon formulation,
solutions will be administered in a manner compatible with the
dosage formulation and in such amount as is therapeutically
effective. The formulations are easily administered in a variety of
dosage forms such as injectable solutions, drug-release capsules,
and the like.
[0313] As used herein, "carrier" includes any and all solvents,
dispersion media, vehicles, coatings, diluents, antibacterial and
antifungal agents, isotonic and absorption delaying agents,
buffers, carrier solutions, suspensions, colloids, and the like.
The use of such media and agents for pharmaceutical active
substances is well known in the art. Except insofar as any
conventional media or agent is incompatible with the active
ingredient, its use in the therapeutic compositions is
contemplated. Supplementary active ingredients can also be
incorporated into the compositions.
[0314] The phrase "pharmaceutically-acceptable" refers to molecular
entities and compositions that do not produce an allergic or
similar untoward reaction when administered to a human. The
preparation of an aqueous composition that contains a protein as an
active ingredient is well understood in the art. Typically, such
compositions are prepared as injectables, either as liquid
solutions or suspensions; solid forms suitable for solution in, or
suspension in, liquid prior to injection can also be prepared. The
preparation can also be emulsified.
[0315] In certain embodiments, the pharmaceutical compositions may
be delivered by intranasal sprays, inhalation, and/or other aerosol
delivery vehicles. Methods for delivering genes, polynucleotides,
and peptide compositions directly to the lungs via nasal aerosol
sprays has been described e.g., in U.S. Pat. No. 5,756,353 and U.S.
Pat. No. 5,804,212 (each specifically incorporated herein by
reference in its entirety). Likewise, the delivery of drugs using
intranasal microparticle resins (Takenaga et al., 1998) and
lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871,
specifically incorporated herein by reference in its entirety) are
also well-known in the pharmaceutical arts. Likewise, transmucosal
drug delivery in the form of a polytetrafluoroetheylene support
matrix is described in U.S. Pat. No. 5,780,045 (specifically
incorporated herein by reference in its entirety).
[0316] In certain embodiments, the delivery may occur by use of
liposomes, nanocapsules, microparticles, microspheres, lipid
particles, vesicles, and the like, for the introduction of the
compositions of the present invention into suitable host cells. In
particular, the compositions of the present invention may be
formulated for delivery either encapsulated in a lipid particle, a
liposome, a vesicle, a nanosphere, a nanoparticle or the like. The
formulation and use of such delivery vehicles can be carried out
using known and conventional techniques.
Kits Comprising Compositions of the Invention
[0317] The invention, in other aspects, provides kits comprising
one or more containers filled with one or more of the polypeptides,
polynucleotides, antibodies, multiunit complexes, compositions
thereof, etc., of the invention, as described herein. The kits can
include written instructions on how to use such compositions (e.g.,
to modulate cellular signaling, angiogenesis, cancer, inflammatory
conditions, etc.).
[0318] The kits herein may also include a one or more additional
therapeutic agents or other components suitable or desired for the
indication being treated. An additional therapeutic agent may be
contained in a second container, if desired. Examples of additional
therapeutic agents include, but are not limited to anti-neoplastic
agents, anti-inflammatory agents, antibacterial agents, antiviral
agents, angiogenic agents, etc.
[0319] The kits herein can also include one or more syringes or
other components necessary or desired to facilitate an intended
mode of delivery (e.g., stents, implantable depots, etc.).
Methods of Use
[0320] Embodiments of the present invention relates to methods of
using substantially monomeric AARS polypeptides and compositions
comprising the same for treating a cell, tissue, or subject in need
thereof. The cells or tissue that may be modulated by the present
invention are preferably mammalian cells, or more preferably human
cells. Such cells can be of a healthy state or of a diseased
state.
[0321] In certain embodiments, for example, methods are provided
for modulating therapeutically relevant cellular activities
including, but not limited to, cellular metabolism, cell
differentiation (e.g., hematopoiesis), cell proliferation, cell
death, cell mobilization, cell migration, gene transcription, mRNA
translation, cell impedance, cytokine production, cytokine receptor
activity, and the like, comprising contacting a cell with an AARS
composition as described herein. The monomeric AARS compositions
may therefore be used in any of a number of therapeutic contexts
including, for example, those relating to the treatment or
prevention of neoplastic diseases, inflammatory conditions, immune
system diseases (e.g., autoimmune diseases and inflammation),
infectious diseases, metabolic diseases, neuronal/neurological
diseases, muscular/cardiovascular diseases, diseases associated
with aberrant hematopoiesis, diseases associated with aberrant
angiogenesis or reduced angiogenesis, diseases associated with
aberrant cell survival, and others.
[0322] In certain embodiments, monomeric AARS polypeptides agonize
CXCR receptors. Certain embodiments therefore relate to methods of
modulating the levels or activity of CXCR-1 or CXCR-2 in a cell,
comprising contacting the cell with monomeric AARS polypeptide
described herein. Certain embodiments include increasing the levels
or activity of CXCR-1 or CXCR-2 in the cell, which may be in a
subject or in vitro. Certain in vivo embodiments include increasing
polymorphonuclear cell (PMNC) migration in the subject.
[0323] Given the role of CXC receptors such as CXCR-1 and CXCR-2
and related chemokines such as IL-8 in modulating inflammatory
responses, in certain illustrative embodiments, the monomeric AARS
compositions of the invention may be used to modulate inflammation
in a subject, e.g., via modulation of cytokine signaling.
Therefore, in related embodiments, the compositions of the
invention may be employed in the treatment of essentially any cell
or tissue or subject that would benefit from modulation of
inflammation. For example, in some embodiments, a cell or tissue or
subject experiencing or susceptible to inflammation, or requiring a
pro-inflammatory response (e.g., an immunosuppressed condition),
may be contacted with a suitable composition of the invention to
stimulate an inflammatory response.
[0324] "Inflammation" refers generally to the biological response
of tissues to harmful stimuli, such as pathogens, damaged cells
(e.g., wounds), and irritants. The term "inflammatory response"
refers to the specific mechanisms by which inflammation is achieved
and regulated, including, merely by way of illustration, immune
cell activation or migration, cytokine production, vasodilation,
including kinin release, fibrinolysis, and coagulation, among
others described herein and known in the art. Ideally, inflammation
is a protective attempt by the body to both remove the injurious
stimuli and initiate the healing process for the affected tissue or
tissues. In the absence of inflammation, wounds and infections
would never heal, creating a situation in which progressive
destruction of the tissue would threaten survival. On the other
hand, excessive or chronic inflammation may associate with a
variety of diseases, such as hay fever, atherosclerosis, and
rheumatoid arthritis, among others described herein and known in
the art.
[0325] Monomeric AARS polypeptides of the invention may modulate
acute inflammation, chronic inflammation, or both. Certain
embodiments relate to increasing acute inflammation or acute
inflammatory responses, and certain embodiments relate to
increasing chronic inflammation or chronic inflammatory responses.
Depending on the needs of the subject, certain embodiments relate
to reducing acute inflammation or inflammatory responses, and
certain embodiments relate to reducing chronic inflammation or
chronic inflammatory responses.
[0326] Acute inflammation relates to the initial response of the
body to presumably harmful stimuli and involves increased movement
of plasma and leukocytes from the blood into the injured tissues.
It is a short-term process, typically beginning within minutes or
hours and ending upon the removal of the injurious stimulus. Acute
inflammation may be characterized by any one or more of redness,
increased heat, swelling, pain, and loss of function. Redness and
heat are due mainly to increased blood flow at body core
temperature to the inflamed site, swelling is caused by
accumulation of fluid, pain is typically due to release of
chemicals that stimulate nerve endings, and loss of function has
multiple causes.
[0327] Acute inflammatory responses are initiated mainly by local
immune cells, such as resident macrophages, dendritic cells,
histiocytes, Kuppfer cells and mastocytes. At the onset of an
infection, burn, or other injuries, these cells undergo activation
and release inflammatory mediators responsible for the clinical
signs of inflammation, such as vasoactive amines and eicosanoids.
Vasodilation and its resulting increased blood flow cause the
redness and increased heat. Increased permeability of the blood
vessels results in an exudation or leakage of plasma proteins and
fluid into the tissue, which creates swelling. Certain released
mediators such as bradykinin increase sensitivity to pain, and
alter the blood vessels to permit the migration or extravasation of
leukocytes, such as neutrophils, which typically migrate along a
chemotactic gradient created by the local immune cells.
[0328] Acute inflammatory responses also includes one or more
acellular biochemical cascade systems, consisting of preformed
plasma proteins modulate, which act in parallel to initiate and
propagate the inflammatory response. These systems include the
complement system, which is mainly activated by bacteria, and the
coagulation and fibrinolysis systems, which are mainly activated by
necrosis, such as the type of tissue damage that is caused by
certain infections, burns, or other trauma. Hence, monomeric AARS
polypeptides may be used to modulate acute inflammation, or any of
one or more of the individual acute inflammatory responses.
[0329] Chronic inflammation, a prolonged and delayed inflammatory
response, is characterized by a progressive shift in the type of
cells that are present at the site of inflammation, and often leads
to simultaneous or near simultaneous destruction and healing of the
tissue from the inflammatory process. At the cellular level,
chronic inflammatory responses involve a variety of immune cells
such as monocytes, macrophages, lymphocytes, plasma cells, and
fibroblasts, though in contrast to acute inflammation, which is
mediated mainly by granulocytes, chronic inflammation is mainly
mediated by mononuclear cells such as monocytes and lymphocytes.
Chronic inflammation also involves a variety of inflammatory
mediators, such as IFN-.gamma. and other cytokines, growth factors,
reactive oxygen species, and hydrolytic enzymes. Chronic
inflammation may last for many months or years, and may result in
undesired tissue destruction and fibrosis.
[0330] Clinical signs of chronic inflammation are dependent upon
duration of the illness, inflammatory lesions, cause and anatomical
area affected. (see, e.g., Kumar et al., Robbins Basic
Pathology-8.sup.th Ed., 2009 Elsevier, London; Miller, L M,
Pathology Lecture Notes, Atlantic Veterinary College,
Charlottetown, PEI, Canada). Chronic inflammation is associated
with a variety of pathological conditions or diseases, including,
for example, allergies, Alzheimer's disease, anemia, aortic valve
stenosis, arthritis such as rheumatoid arthritis and
osteoarthritis, cancer, congestive heart failure, fibromyalgia,
fibrosis, heart attack, kidney failure, lupus, pancreatitis,
stroke, surgical complications, inflammatory lung disease,
inflammatory bowel disease, atherosclerosis, and psoriasis, among
others described herein and known in the art. Hence, monomeric AARS
polypeptides may be used to treat or manage chronic inflammation,
modulate any of one or more of the individual chronic inflammatory
responses, or treat any one or more diseases or conditions
associated with chronic inflammation.
[0331] Monomeric AARS polypeptides may also modulate proliferative
inflammation, an inflammatory process characterized by an increase
in the number of tissue cells. These can encompass skin conditions
such as psoriasis, seborrhea or eczema, or can also be thought of
in terms of cancers and abnormal growths especially in light of
accumulating evidence based on more efficient molecular methods to
document even low grade chronic inflammation.
[0332] In certain embodiments, monomeric AARS polypeptides may
modulate inflammatory responses at the cellular level, such as by
modulating the activation, inflammatory molecule secretion (e.g.,
cytokine or kinin secretion), proliferation, activity, migration,
or adhesion of various cells involved in inflammation. Examples of
such cells include immune cells and vascular cells. Immune cells
include, for example, granulocytes such as neutrophils, eosinophils
and basophils, macrophages/monocytes, lymphocytes such as B-cells,
killer T-cells (i.e., CD8+ T-cells), helper T-cells (i.e., CD4+
T-cells, including T.sub.h1 and T.sub.h2 cells), natural killer
cells, .gamma..delta. T-cells, dendritic cells, and mast cells.
Examples of vascular cells include smooth muscle cells, endothelial
cells, and fibroblasts. Also included are methods of modulating an
inflammatory condition associated with one or more immune cells or
vascular cells, including neutrophil-mediated, macrophage-mediated,
and lymphocyte-mediated inflammatory conditions. In certain
embodiments, monomeric AARS polypeptides increase the levels,
migration, or recruitment of PMNCs such as neutrophils, basophils,
and eosinophils.
[0333] In certain embodiments, monomeric AARS polypeptides may
modulate the levels or activity of inflammatory molecules,
including plasma-derived inflammatory molecules and cell-derived
inflammatory molecules. Included are pro-inflammatory molecules and
anti-inflammatory molecules. Examples of plasma-derived
inflammatory molecules include, without limitation, proteins or
molecules of any one or more of the complement system, kinin
system, coagulation system, and the fibrinolysis system. Examples
of members of the complement system include C1, which exists in
blood serum as a molecular complex containing about 6 molecules of
C1q, 2 molecules of C1r, and 2 molecules of C1s, C2 (a and b), C3
(a and B), C4 (a and b), C5, and the membrane attack complex of
C5a, C5b, C6, C7, C8, and C9. Examples of the kinin system include
bradykinin, kallidin, kallidreins, carboxypeptidases,
angiotensin-converting enzyme, and neutral endopeptidase.
[0334] Examples of cell-derived inflammatory molecules include,
without limitation, enzymes contained within lysosome granules,
vasoactive amines, eicosanoids, cytokines, acute-phase proteins,
and soluble gases such as nitric oxide. Vasoactive amines contain
at least one amino group, and target blood vessels to alter their
permeability or cause vasodilation. Examples of vasoactive amines
include histamine and serotonin. Eicosanoids refer to signaling
molecules made by oxidation of twenty-carbon essential fatty acids,
and include prostaglandins, prostacyclins, thromboxanes, and
leukotrienes.
[0335] Cytokines refer to a variety of substances that are secreted
by immune cells, and include polypeptides and glycoproteins.
Typically, cytokines are categorized as either autocrine cytokines,
which act on the same type of cell from which the cytokine is
secreted, or paracrine cytokines, which are restricted to acting on
a different cell type from which the cytokine is secreted.
[0336] Each cytokine typically has a corresponding cytokine
receptor. Examples of classes of cytokine receptors include,
without limitation, receptors from the immunoglobulin (Ig)
superfamily, such as the IL-1 receptor types, which share
structural homology with immunoglobulins (antibodies), cell
adhesion molecules, and even some cytokines, and receptors from the
hematopoietic growth factor family, such as the IL-2 receptor
family and the receptors for GM-CSF, IL-3, and IL-5, receptors from
the interferon (type 2) family, including receptors for IFN .beta.
and .gamma.. Additional examples include receptors from the tumor
necrosis factors (TNF) (type 3) family, which share a cysteine-rich
common extracellular binding domain and interact with several other
non-cytokine ligands such as CD40, CD27 and CD30, receptors from
the seven transmembrane helix family, including G-protein coupled
receptors, and chemokine receptors such as CXCR-1, CXCR-2, CXCR4
and CCR5, as well as receptors for IL-8, MIP-1 and RANTES. Hence,
in certain embodiments, monomeric AARS polypeptides may modulate
the levels or activity of one or more selected cytokines, the
levels or activity of one or more selected cytokine receptors, the
interaction between cytokines and their receptors, or any
combination thereof.
[0337] Monomeric AARS polypeptides may also modulate levels or
activity of acute-phase proteins. Examples of acute-phase proteins
include C-reactive protein, serum amyloid A, serum amyloid P, and
vasopressin. In certain instances, expression of acute-phase
proteins can cause a range of undesired systemic effects including
amyloidosis, fever, increased blood pressure, decreased sweating,
malaise, loss of appetite, and somnolence. Accordingly, monomeric
AARS polypeptides may modulate the levels or activity of
acute-phase proteins, their systemic effects, or both.
[0338] In certain embodiments, monomeric AARS polypeptides modulate
local inflammation, systemic inflammation, or both. In certain
embodiments, monomeric AARS polypeptides may increase or maintain
(i.e., prevent further reductions) local inflammation or local
inflammatory responses. In certain embodiments, depending on the
needs of the subject, monomeric AARS polypeptides may increase
systemic inflammation or systemic inflammatory responses.
[0339] In certain embodiments, the modulation of inflammation or
inflammatory responses can be associated with one or more tissues
or organs. Non-limiting examples of such tissues or organs include
skin (e.g., dermis, epidermis, subcutaneous layer), hair follicles,
nervous system (e.g., brain, spinal cord, peripheral nerves),
auditory system or balance organs (e.g., inner ear, middle ear,
outer ear), respiratory system (e.g., nose, trachea, lungs),
gastroesophogeal tissues, the gastrointestinal system (e.g., mouth,
esophagus, stomach, small intestines, large intestines, rectum),
vascular system (e.g., heart, blood vessels and arteries), liver,
gallbladder, lymphatic/immune system (e.g., lymph nodes, lymphoid
follicles, spleen, thymus, bone marrow), uro-genital system (e.g.,
kidneys, ureter, bladder, urethra, cervix, Fallopian tubes,
ovaries, uterus, vulva, prostate, bulbourethral glands, epidiymis,
prostate, seminal vesicles, testicles), musculoskeletal system
(e.g., skeletal muscles, smooth muscles, bone, cartilage, tendons,
ligaments), adipose tissue, mammaries, and the endocrine system
(e.g., hypothalamus, pituitary, thyroid, pancreas, adrenal glands).
Accordingly, monomeric AARS polypeptides may be used to modulate
inflammation associated with any of these tissues or organs, such
as to treat conditions or diseases that are associated with the
inflammation of these tissues or organs.
[0340] Certain embodiments may employ monomeric AARS polypeptides
to increase inflammation. For instance, depending on the needs of
the subject, certain embodiments may increase acute inflammation or
increase acute inflammatory responses or both. Certain embodiments
may increase chronic inflammation or chronic inflammatory responses
or both. Certain embodiments may increase both acute and chronic
inflammation. Certain embodiments may increase local or systemic
inflammation or both. These and related embodiments may be useful
for treating or managing conditions associated with reduced
inflammation or insufficient inflammatory responses.
[0341] In certain embodiments, monomeric AARS polypeptides may be
used to treat or manage immunodeficiencies, including primary
immunodeficiencies and secondary immunodeficiencies, in which the
body may not mount an adequate inflammatory response. Examples of
primary immunodeficiencies include various autosomal recessive and
X-linked genetic conditions such as T-cell and B-cell
immunodeficiencies, including combined T-cell and B-cell
immunodeficiencies, antibody deficiencies, well-defined syndromes,
immune dysregulation diseases, phagocyte disorders, innate immunity
disorders, and complement deficiencies.
[0342] Examples of T-cell and B-cell immunodeficiencies include
T-/B+ deficiencies such as .gamma.c deficiency, JAK3 deficiency,
interleukin 7 receptor chain .alpha. deficiency, CD45 deficiency,
CD3.delta./CD3.epsilon. deficiency; and T-/B- deficiencies such as
RAG 1/2 deficiency, DCLRE1C deficiency, adenosine deaminase (ADA)
deficiency, reticular dysgenesis. Additional examples include Omenn
syndrome, DNA ligase type IV deficiency, CD40 ligand deficiency,
CD40 deficiency, purine nucleoside phosphorylase (PNP) deficiency,
MHC class II deficiency, CD3.gamma. deficiency, CD8 deficiency,
ZAP-70 deficiency, TAP-1/2 deficiency, and winged helix
deficiency.
[0343] Examples of antibody deficiencies include X-linked
agammaglobulinemia (btk deficiency, or Bruton's
agammaglobulinemia), .mu.-Heavy chain deficiency, 1-5 deficiency,
Ig.alpha. deficiency, BLNK deficiency, thymoma with
immunodeficiency, common variable immunodeficiency (CVID), ICOS
deficiency, CD19 deficiency, TACI (TNFRSF13B) deficiency, and BAFF
receptor deficiency. Additional examples include AID deficiency,
UNG deficiency, heavy chain deletions, kappa chain deficiency,
isolated IgG subclass deficiency, IgA with IgG subclass deficiency,
selective immunoglobulin A deficiency, and transient
hypogammaglobulinemia of infancy (THI).
[0344] Examples of "well-defined syndromes" include Wiskott-Aldrich
syndrome, ataxia telangiectasia, ataxia-like syndrome, Nijmegen
breakage syndrome, Bloom syndrome, DiGeorge syndrome,
immuno-osseous dysplasias such as cartilage-hair hypoplasia,
Schimke syndrome, Hermansky-Pudlak syndrome type 2, Hyper-IgE
syndrome, chronic mucocutaneous candidiasis.
[0345] Examples of immune dysregulation diseases include
immunodeficiency with hypopigmentation or albinism such as
Chediak-Higashi syndrome and Griscelli syndrome type 2, familial
hemophagocytic lymphohistiocytosis such as perforin deficiency,
MUNC13D deficiency, and syntaxin 11 deficiency, X-linked
lymphoproliferative syndrome, autoimmune lymphoproliferative
syndrome such as type 1a (CD95 defects), type 1b (Fas ligand
defects), type 2a (CASP10 defects), and type 2b (CASP8 defects),
autoimmune polyendocrinopathy with candidiasis and ectodermal
dystrophy, and immunodysregulation polyendocrinopathy enteropathy
X-linked syndrome. Additionally, diseases affecting the bone marrow
may result in abnormal or few leukocytes, such as leukopenia.
Leukopenia can be induced by certain infections and diseases,
including viral infection, Rickettsia infection, some protozoa,
tuberculosis, and certain cancers.
[0346] Examples of phagocyte disorders include severe congenital
neutropenia such as ELA2 deficiency (e.g., with myelodysplasia),
GFI1 deficiency (with T/B lymphopenia) or G-CSFR deficiency
(G-CSF-unresponsive), Kostmann syndrome, cyclic neutropenia,
X-linked neutropenia/myelodysplasia, leukocyte adhesion deficiency
types 1, 2 and 3, RAC2 deficiency, .beta.-actin deficiency,
localized juvenile periodontitis, Papillon-Lefevre syndrome,
specific granule deficiency, Shwachman-Diamond syndrome, chronic
granulomatous disease, including X-linked and autosomal forms,
neutrophil glucose-6-phosphate dehydrogenase deficiency, IL-12 and
IL-23 .beta.1 chain deficiency, IL-12p40 deficiency, interferon
.gamma. receptor 1 deficiency, interferon .gamma. receptor 2
deficiency, and STAT1 deficiency.
[0347] Examples of innate immunity deficiencies include
hypohidrotic ectodermal dysplasia such as NEMO deficiency and IKBA
deficiency, IRAK-4 deficiency, WHIM syndrome (warts,
hypogammaglobulinaemia, infections, myleokathexis), and
epidermodysplasia verruciformis. Examples of complement
deficiencies and exemplary associated conditions include C1q
deficiency (e.g., lupus-like syndrome, rheumatoid disease,
infections), C1r deficiency, C4 deficiency, C2 deficiency (e.g.,
lupus-like syndrome, vasculitis, polymyositis, pyogenic
infections), C3 deficiency (e.g., recurrent pyogenic infections),
C5 deficiency (e.g., neisserial infections), C6 deficiency, C7
deficiency (e.g., vasculitis), C8a and C8b deficiency, C9
deficiency (e.g., neisserial infections), C1-inhibitor deficiency
(e.g., hereditary angioedema), Factor I deficiency (pyogenic
infections), Factor H deficiency (e.g., haemolytic-uraemic
syndrome, membranoproliferative glomerulonephritis), Factor D
deficiency (e.g., neisserial infections), Properdin deficiency
(e.g., neisserial infections), MBP deficiency (e.g., pyogenic
infections), and MASP2 deficiency.
[0348] Primary immune deficiencies can be diagnosed according to
routine techniques in the art. Exemplary diagnostic tests include,
without limitation, performing counts of the different types of
mononuclear cells in the blood (e.g., lymphocytes and monocytes,
including lymphocytes, different groups of B lymphocytes such as
CD19+, CD20+, and CD21+ lymphocytes, natural killer cells, and
monocytes positive for CD15+), measuring the presence of activation
markers (e.g., HLA-DR, CD25, CD80), performing tests for T cell
function such as skin tests for delayed-type hypersensitivity, cell
responses to mitogens and allogeneic cells, cytokine production by
cells, performing tests for B cell function such as by identifying
antibodies to routine immunizations and commonly acquired
infections and by quantifying IgG subclasses, and performing tests
or phagocyte function, such as by measuring the reduction of nitro
blue tetrazolium chloride, and performing assays of chemotaxis and
bactericidal activity. Monomeric AARS polypeptides may therefore be
used to stimulate or maintain acute inflammation or acute
inflammatory responses in subjects with a primary immunodeficiency,
as described herein and known in the art.
[0349] Examples of causes of secondary immunodeficiencies include
malnutrition, aging, and medications (e.g., chemotherapy,
disease-modifying anti-rheumatic drugs, immunosuppressive drugs
after organ transplants, glucocorticoids). Additional causes
include various cancers, including cancers of the bone marrow and
blood cells (e.g., leukemia, lymphoma, multiple myeloma), and
certain chronic infections, such as acquired immunodeficiency
syndrome (AIDS), caused by the human immunodeficiency virus (HIV).
Monomeric AARS polypeptides may be used to stimulate or maintain
acute inflammation or acute inflammatory responses in subjects with
an immunodeficiency, as described herein and known in the art.
Monomeric AARS polypeptides may also be used to stimulate or
maintain chronic inflammation or chronic inflammatory responses in
subjects with a secondary immunodeficiency, as described herein and
known in the art.
[0350] Monomeric AARS polypeptides may also be employed to treat or
manage idiopathic inflammation or inflammation of unknown etiology.
Also included are combination therapies, in which one or more
monomeric AARS polypeptides are administered or utilized in
combination with one or more other therapies for any of the
inflammatory diseases or conditions described herein, including
those therapies that are commonly available and known in the art.
Examples of combination therapies include the use of standard
anti-inflammatory agents such as non-steroidal anti-inflammatory
drugs (NSAIDs), immune selective anti-inflammatory derivatives
(ImSAIDs), and steroids (e.g., corticosteroids), anti-infectives
such as antibiotics and anti-viral agents, anti-oxidants,
cytokines, chemotherapeutic agents and other anti-cancer therapies,
and immunosuppressive therapies.
[0351] Criteria for assessing the signs and symptoms of
inflammatory and other conditions, including for purposes of making
differential diagnosis and also for monitoring treatments such as
determining whether a therapeutically effective dose has been
administered in the course of treatment, e.g., by determining
improvement according to accepted clinical criteria, will be
apparent to those skilled in the art and are exemplified by the
teachings of e.g., Berkow et al., eds., The Merck Manual, 16.sup.th
edition, Merck and Co., Rahway, N.J., 1992; Goodman et al., eds.,
Goodman and Gilman's The Pharmacological Basis of Therapeutics,
10.sup.th edition, Pergamon Press, Inc., Elmsford, N.Y., (2001);
Avery's Drug Treatment: Principles and Practice of Clinical
Pharmacology and Therapeutics, 3rd edition, ADIS Press, Ltd.,
Williams and Wilkins, Baltimore, Md. (1987); Ebadi, Pharmacology,
Little, Brown and Co., Boston, (1985); Osolci al., eds.,
Remington's Pharmaceutical Sciences, 18.sup.th edition, Mack
Publishing Co., Easton, Pa. (1990); Katzung, Basic and Clinical
Pharmacology, Appleton and Lange, Norwalk, Conn. (1992).
[0352] As noted above, in certain illustrative embodiments, the
monomeric AARS compositions of the invention may be used to
modulate angiogenesis, e.g., via modulation of endothelial cell
proliferation and/or signaling. Endothelial cell proliferation
and/or cell signaling may be monitored using an appropriate cell
line (e.g., Human microvascular endothelial lung cells (HMVEC-L)
and Human umbilical vein endothelial cells (HUVEC)), and using an
appropriate assay (e.g., endothelial cell migration assays,
endothelial cell proliferation assays, tube-forming assays,
matrigel plug assays, etc.), many of which are known and available
in the art.
[0353] Therefore, in related embodiments, the compositions of the
invention may be employed in the treatment of essentially any cell
or tissue or subject that would benefit from modulation of
angiogenesis. For example, in some embodiments, a cell or tissue or
subject experiencing or susceptible to angiogenesis (e.g., an
angiogenic condition) may be contacted with a suitable composition
of the invention to inhibit an angiogenic condition.
[0354] Certain embodiments include methods of reducing
cadherin-mediated cell-cell adhesion, comprising contacting one or
more cells with substantially monomeric AARS polypeptide described
herein. Also included are methods of modulating the levels,
phosphorylation state, or a biological activity of VE-cadherin in a
cell, comprising contacting the cell with substantially monomeric
AARS polypeptide. Certain embodiments include reducing the levels
of VE-cadherin in the cell, which may be in a subject. Certain
embodiments include reducing the levels of circulating VE-cadherin
in the host, which has been associated with various cancers (see,
e.g., Rabascio et al., Cancer Research 64:4373-4377, 2004).
[0355] Certain embodiments include reducing the phosphorylation of
VE-cadherin at one or more tyrosine residues, and certain
embodiments include reducing the biological activity of
VE-cadherin. Examples of VE-cadherin-related biological activities
include the ability to associate with, or promote the signaling of,
vascular endothelial cell growth factor receptor (VEGFR2), and the
ability of one or more VE-cadherin polypeptides to self-assemble,
or to associate with other VE-cadherin polypeptides. In certain
embodiments, the substantially monomeric AARS polypeptides directly
bind to VE-cadherin and thereby reduce its biological activity.
[0356] Given the role of cadherins such as VE-cadherin in
regulating various biological processes, the AARS polypeptides of
the present invention may be used for modulating cadherin-mediated
activities in a subject. One example of a cadherin-mediated
activity is angiogenesis, which is mediated by VE-cadherin. Other
examples include regulating the growth or development of neural
tissues, placental tissues, vascular tissues, epithelial tissues,
retinal tissues, renal tissues, muscle tissues, liver tissues,
intestinal tissues, and bone tissues.
[0357] In certain embodiments, as noted above, the monomeric AARS
polypeptides provided herein may reduce angiogenesis, such as by
disrupting the formation or activity of VE-cadherin homophilic
complexes, and thereby reducing their angiogenesis stimulating
activity. Other mechanisms include disrupting the angiogenic
signaling of other proteins or ligands, such as angiogenic
aminoacyl-tRNA synthetases, including dimeric AARS polypeptides.
Given also the role of CXC receptors such as CXCR-2 and CXCR-2 and
related chemokines such as IL-8 in modulating angiogenesis, in
certain embodiments, the monomeric AARS polypeptides provided
herein that agonize their activity may modulate or increase
angiogenesis, e.g., via modulation of cytokine signaling.
[0358] "Angiogenesis" refers generally to the growth of new
capillary blood vessels, whether in vivo or in vitro, and may
include any one or more of the growth of new blood vessels from
pre-existing vessels (i.e., sprouting angiogenesis), spontaneous
blood-vessel formation (i.e., vasculogenesis), new blood vessel
formation by the splitting of an existing vessel (i.e., splitting
angiogenesis), or the formation of medium-sized blood vessels
possessing tunica media plus adventitia (i.e., arteriogenesis).
[0359] Sprouting angiogenesis occurs in well-defined stages. First,
angiogenic growth factors activate endothelial cells in
pre-existing blood vessels via certain cell-surface receptors. The
activated endothelial cells then release proteases to degrade the
basement membrane, allowing them to migrate from the parent vessel
wall. The endothelial cells then proliferate into the surrounding
matrix and form solid sprouts to connect with neighboring vessels.
As these sprouts extend toward the source of the angiogenic
stimulus, endothelial cells migrate in tandem, using adhesion
molecules such as integrins. As cells migrate to the site of
angiogenesis, these sprouts then form loops to generate a
full-fledged vessel lumen.
[0360] Splitting angiogenesis also occurs in well-defined stages.
First, two opposing vessel walls establish a zone of contact, after
which the endothelial cell junctions are reorganized and the vessel
bilayer is perforated to allow growth factors and cells to
penetrate into the lumen. Then, a core of pericytes and
myofibroblasts is formed between the two new vessels at the zone of
contact. The cells in this core then begin laying collagen fibers
into the core to provide an extracellular matrix for growth of the
vessel lumen. Finally, the core is fleshed out with little or no
alterations to the basic structure.
[0361] In certain embodiments, the modulation (i.e., stimulation or
reduction) of angiogenesis can be associated with one or more
tissues or organs. Non-limiting examples of such tissues or organs
include skin (e.g., dermis, epidermis, subcutaneous layer), hair
follicles, nervous system (e.g., brain, spinal cord, peripheral
nerves), auditory system or balance organs (e.g., inner ear, middle
ear, outer ear), respiratory system (e.g., nose, trachea, lungs),
gastroesophogeal tissues, the gastrointestinal system (e.g., mouth,
esophagus, stomach, small intestines, large intestines, rectum),
vascular system (e.g., heart, blood vessels and arteries), liver,
gallbladder, lymphatic/immune system (e.g., lymph nodes, lymphoid
follicles, spleen, thymus, bone marrow), uro-genital system (e.g.,
kidneys, ureter, bladder, urethra, cervix, Fallopian tubes,
ovaries, uterus, vulva, prostate, bulbourethral glands, epidiymis,
prostate, seminal vesicles, testicles), musculoskeletal system
(e.g., skeletal muscles, smooth muscles, bone, cartilage, tendons,
ligaments), adipose tissue, mammaries, and the endocrine system
(e.g., hypothalamus, pituitary, thyroid, pancreas, adrenal glands).
Accordingly, the monomeric AARS polypeptides provided herein may be
used to modulate angiogenesis, including aberrant angiogenesis,
associated with any of these tissues or organs. Examples include
the treatment of conditions associated with inflammation or cancer
of these tissues or organs, or conditions associated with an
insufficient angiogenic response.
[0362] As noted above, cadherins such as VE-cadherin play a central
role in stimulating angiogenesis. Certain monomeric AARS
polypeptides may therefore be employed to treat or manage
conditions associated with aberrant or increased angiogenesis.
Examples of conditions associated with aberrant angiogenesis
include, without limitation, cancer, coronary heart disease, tumor
metastasis, inflammatory vascular disease, inflammation,
ischemia-reperfusion injury, hypertension, rheumatoid arthritis,
diabetic retinopathy, macular degeneration, and diabetes, in
addition to others described herein.
[0363] Certain monomeric AARS polypeptides provided herein may be
used in treating cancer. Cancer refers to the uncontrolled growth
of abnormal cells in the body. In certain embodiments cancerous
cells include malignant cells. Most if not all cancerous tumors,
for example, release angiogenic growth factor proteins that
stimulate blood vessels to grow into the tumor, providing it with
oxygen and nutrients. Anti-angiogenic therapies starve the tumor of
its blood supply by interfering with this process.
[0364] Cancer as used herein refers to the uncontrolled growth of
abnormal cells in the body. In certain embodiments cancerous cells
include malignant cells. Examples of cancers include, without
limitation, prostate cancer, breast cancer, colon cancer, rectal
cancer, lung cancer, ovarian cancer, testicular cancer, stomach
cancer, bladder cancer, pancreatic cancer, liver cancer, kidney
cancer, brain cancer, melanoma, non-melanoma skin cancer, bone
cancer, lymphoma, leukemia, thyroid cancer, endometrial cancer,
multiple myeloma, acute myeloid leukemia, neuroblastoma, and
glioblastoma. Also included is Kaposi's sarcoma, in which lesions
result in part from abnormal growth of blood vessels. Certain
embodiments include treating metastatic forms of these cancers, or
cancers that have spread (metastasizes) from their original site to
another area of the body. Also included are conditions such as
hemangiomas, colon polyps, and precancerous skin lesions.
[0365] The methods provided herein can also be applied to cancers
of the blood and lymphatic systems, including lymphomas, leukemia,
and myelomas. Examples of specific cancers that may be treated
according to the invention include, but are not limited to,
Hodgkin's and non-Hodgkin's Lymphoma (NHL), including any type of
NHL as defined according to any of the various classification
systems such as the Working formulation, the Rappaport
classification and, preferably, the REAL classification. Such
lymphomas include, but are not limited to, low-grade,
intermediate-grade, and high-grade lymphomas, as well as both
B-cell and T-cell lymphomas. Included in these categories are the
various types of small cell, large cell, cleaved cell, lymphocytic,
follicular, diffuse, Burkitt's, Mantle cell, NK cell, CNS,
AIDS-related, lymphoblastic, adult lymphoblastic, indolent,
aggressive, transformed and other types of lymphomas. Examples of
specific myeloproliferative disorders that may be treated according
to methods of the present invention include, e.g., polycythemia
vera, essential thrombocythemia, agnogenic myeloid metaplasia,
myelofibrosis, myelodysplastic syndrome, and chronic myelocytic
leukemia. The methods of the present invention can be used for
adult or childhood forms of lymphoma, as well as lymphomas at any
stage, e.g., stage I, II, III, or IV.
[0366] Certain embodiments may reduce the proliferation of one or
more cancer cells. Certain embodiments may reduce the metastases or
spread of one or more cancer cells. Certain embodiments may
increase the migration of PMNCs or leukocytes to the tumor site.
Certain embodiments may reduce tumor size. Certain embodiments may
reduce or manage the clinical symptoms associated with one or more
cancers, such as pain, chills, fatigue, fever, loss of appetite,
malaise, night sweats, and weight loss.
[0367] In certain embodiments, the monomeric AARS polypeptides
provided herein may be administered as first line treatments or as
secondary treatments, as an adjunct to various cancer treatments.
Examples of cancer treatments include surgery, radiation therapy,
chemotherapy, targeted therapies, immunotherapy, hormonal therapy,
stem-cell therapies, bone marrow replacement therapies, symptom
control, complementary or alternative therapies, or others. In
addition, they may be administered as a primary chemotherapeutic
treatment or as adjuvant or neoadjuvant chemotherapy.
[0368] The monomeric AARS polypeptides provided herein may be used
in combination therapies with chemotherapeutic agents. Examples of
chemotherapeutic agents that may be administered as combination
therapies include chlorambucil, cyclophosphamide, lomustine (CCNU),
melphalan, procarbazine, thiotepa, carmustine (BCNU), busulfan,
daunorubicin, doxorubicin, idarubicin, epirubicin, mitoxantrone,
bleomycin, cisplatin, carboplatin, oxaliplatin, camptothecins,
irinotecan, topotecan, amsacrine, etoposide, etoposide phosphate,
teniposide, vincristine, vinblastine, vinorelbine, vindesine,
paclitaxel, mechlorethamine, ifosfamide, nitrosurea, dactinomycin,
plicomycin, mitomycin, tamoxifen, raloxifene, estrogen receptor
binding agents, gemcitabien, navelbine, farnesyl-protein
transferase inhibitors, transplatinum, 5-fluorouracil,
methotrexate, and temazolomide. Examples of cancer-related
transplant therapies that may be used in conjunction with the
monomeric AARS polypeptides provided herein include bone marrow
transplants, cord blood transplants, hematopoietic stem cell
transplants, and autologous peripheral blood cell progenitor
transplants, among others.
[0369] Also included are methods of modulating angiogenesis
associated with infections, including bacterial, viral, and
parasitic infections. As one example, Verruga peruana is a clinical
syndrome caused by the bacterium Bartonella bacilliformis, and is
characterized by the development of hemangioma-like lesions, in
which bacteria colonize endothelial cells. High-level expression of
angiopoietin-2 and VEGF receptors has been observed in the
endothelium of verruga peruana, and infection of cultured
endothelium with B. bacilliformis results in induction of
angiopoetin-2 in vitro, demonstrating a collaboration between
infected endothelium and overlying epidermis to induce
angiogenesis. Hence, the monomeric AARS polypeptides provided
herein may reduce the angiogenesis associated with this and similar
bacteria.
[0370] As a further example, human cytomegalovirus (HCMV) infection
is associated with atherosclerosis, transplant vascular sclerosis,
and coronary restenosis. A common theme in these vascular diseases
is an increased rate of angiogenesis. HCMV infection results in
increased EC proliferation, motility, and capillary tube formation.
HCMV-induced angiogenic response depends on viral binding to and
signaling through the .beta..sub.1, and .beta..sub.3 integrins and
the epidermal growth factor receptor, via their ability to activate
the phosphatidylinositol 3-kinase and the mitogen-activated protein
kinase signaling pathways. Since a proangiogenic response drives
the neovascularization observed in atherosclerotic disease, HCMV
infection may contribute to vascular disease by inducing
angiogenesis. Hence, the monomeric AARS polypeptides provided
herein may reduce the angiogenesis associated with this and similar
viruses. The monomeric AARS polypeptides provided herein may be
used to reduce the angiogenesis associated with one or more
infectious agents, either alone or in combination with
anti-infective agents.
[0371] Exemplary parasites that induce angiogenesis include
parasitic nematodes such as Trichinella spiralis and Onchocerca
volvulus, and helminth parasites such as Schistosoma mansoni.
Hence, the monomeric AARS polypeptides provided herein may reduce
the angiogenesis associated with this and similar parasites.
[0372] Further illustrative examples of angiogenic conditions
include, but are not limited to, age-related macular degeneration
(AMD), cancer (both solid and hematologic), developmental
abnormalities (organogenesis), diabetic blindness, endometriosis,
ocular neovascularization, psoriasis, rheumatoid arthritis (RA),
and skin discolorations (e.g., hemangioma, nevus flammeus or nevus
simplex).
[0373] As noted above, chemokines such as IL-8 and CXC receptors
such CXCR-1 and CXCR-2 play a role in stimulating angiogenesis.
Certain monomeric AARS polypeptides, which agonize CXCR-1 and
CXCR-2, may therefore be employed as pro-angiogenic agents to treat
or manage conditions associated with reduced angiogenesis. Examples
of conditions associated with reduced angiogenesis or that could
benefit from pro-angiogenic treatment include, without limitation,
cardiovascular disease, restenosis, tissue damage after reperfusion
of ischemic tissue or cardiac failure, chronic inflammation and
wound healing.
[0374] The monomeric AARS polypeptides provided herein may
therefore be useful in the treatment of vascular or cardiovascular
diseases or conditions. Examples include coronary artery disease,
coronary heart disease, peripheral arterial disease, wound healing,
ischemic-reperfusion injury such as stroke, and others. Also
included are atherosclerosis, stenosis, restenosis such as coronary
restenosis, and transplant vascular sclerosis. In certain
embodiments, stenosis may occur after a coronary artery bypass
graft (CABG) operation. In certain embodiments, restenosis may
occur after angioplasty, vascular surgery, cardiac surgery, or
other treatment to clear arterial blockage, including blockage in
the coronary or peripheral arteries.
[0375] Monomeric AARS polypeptides may be employed in the treatment
of physical injuries or wounds. Examples include abrasions,
bruises, cuts, puncture wounds, lacerations, impact wounds,
concussions, contusions, thermal burns, frostbite, chemical burns,
sunburns, gangrene, necrosis, desiccations, radiation burns,
radioactivity burns, smoke inhalation, torn muscles, pulled
muscles, torn tendons, pulled tendons, pulled ligaments, torn
ligaments, hyperextensions, torn cartilage, bone fractures, pinched
nerves, ulcers, and gunshot or other traumatic wounds.
[0376] As a further illustrative example, and without wishing to be
bound by any one theory, certain AARS polypeptides (e.g., monomeric
YRS) agonize CXC receptors, similar to IL-8, and IL-8 has been
shown to induce the regression of macroscopic tumors in a model of
peritoneal carcinomatosis in the rat. In this model, IL-8 was shown
to recruit PMNCs to the challenge site but did not enhance PMNC
infiltration of the tumor or the cytotoxic activity of PMNCs.
Regardless, IL-8 did have significant therapeutic activity which
may be secondary to PMNC cytotoxicity and associated with other
intermediate cells. It was suggested, for example, that lymphocytes
were involved since IL-8 has also demonstrated the ability to
stimulate T-cell chemotaxisis. (Lejeune et al, Cancer Immunol
Immunotherapy. 38:167-170, 1994). Because certain monomeric AARS
polypeptides agonize CXCR-1 and CXCR-2 and stimulate PMNC
migration, similar to the activity of IL-8, they may likewise
possess anti-cancer therapeutic activity. Accordingly, certain AARS
polypeptides that stimulate angiogenesis may be useful in treating
cancers, as described herein.
[0377] Also included are methods of increasing angiogenesis as a
method of treating various infections, including bacterial, viral,
and parasitic infections. Without wishing to be bound by any on
theory, it is believed that similarly acting chemokines such as
interleukin-8 have shown anti-infective therapeutic activity. For
example, interleukin-8 has shown therapeutic activity in
non-neutropenic mice that received IL-8 shortly before challenge
and at the site of infectious challenge with either P. aeruginosa,
Klebsiella pneumoniae, or Plasmodium berghei (see, e.g., Vogels et
al., Antimicrob-Agents-Chemother. 37:276-280, 1993). Monomer AARS
polypeptides, which agonize CXCR-1 and CXCR-2, may thus be employed
in certain instances as an anti-infective, alone or in combination
with standard anti-infectives, such as antibiotics, anti-virals,
and other anti-microbial agents.
[0378] In still further embodiments, the compositions of the
invention may be used in the treatment of neuronal/neurological
diseases or disorders, illustrative examples of which include
Parkinson's disease, Alzheimer's disease, Pick's disease,
Creutzfeldt-Jacob disease, Huntington's chorea, alternating
hemiplegia, amyotrophic lateral sclerosis, ataxia, cerebral palsy,
chronic fatigue syndrome, chronic pain syndromes, congenital
neurological anomalies, cranial nerve diseases, delirium, dementia,
demyelinating diseases, dysautonomia, epilepsy, headaches,
Huntington's disease, hydrocephalus, meningitis, movement
disorders, muscle diseases, nervous system neoplasms,
neurocutaneous syndromes, neurodegenerative diseases, neurotoxicity
syndromes, ocular motility disorders, peripheral nervous system
disorders, pituitary disorders, porencephaly, Rett syndrome, sleep
disorders, spinal cord disorders, stroke, sydenham's chorea,
tourette syndrome, nervous system trauma and injuries, etc.
[0379] Furthermore, additional embodiments relate to the use of the
compositions of the invention in the treatment of metabolic
disorders such as adrenoleukodystrophy, Krabbe's disease (globoid
cell leukodystrophy), metachromatic leukodystrophy, Alexander's
disease, Canavan's disease (spongiform leukodystrophy),
Pelizaeus-Merzbacher disease, Cockayne's syndrome, Hurler's
disease, Lowe's syndrome, Leigh's disease, Wilson's disease,
Hallervorden-Spatz disease, Tay-Sachs disease, etc. The utility of
the compositions of the invention in modulating angiogenic or
metabolic processes may be monitored using any of a variety of
techniques known and available in the art including, for example,
assays which measure adipocyte lipogenesis or adipocyte
lipolysis.
[0380] In more specific embodiments of the invention, the monomeric
AARS compositions of the invention may be used to modulate cellular
signaling, for example, via cell signaling proteins such as
chemokines or chemokine receptors, including CXCR-1 and CXCR-2, or
cadherins such as VE-cadherin. Cell signaling may be monitored
using any of a number of well known assays. Detection of cell
signaling activities in response to treatment of cells with
monomeric AARS polypeptides therefore serves as an indicator of
distinct biological effects. Target proteins used for this assay
may be selected so as to encompass key components of major cellular
signaling cascades, thereby providing a broad picture of the cell
signaling landscape and its therapeutic relevance. In certain
embodiments, such assays involve cell treatment with monomeric AARS
polypeptides followed by immunodetection with antibodies that
specifically detect the levels of phosphorylated or
un-phosphorylated forms of the target proteins.
[0381] Of course, it will be recognized that other classes of
proteins, such as cell adhesion molecules (e.g., cadherins,
integrins, claudins, catenins, selectins, etc.) and/or ion channel
proteins may also be assayed for monitoring cellular events or
activities modulated by the compositions of the invention.
[0382] Generally, a therapeutically effective amount of polypeptide
is administered to a subject or patient. In particular embodiments,
the amount of polypeptide administered will typically be in the
range of about 0.1 .mu.g/kg to about 0.1 mg/kg to about 50 mg/kg of
patient body weight. Depending on the type and severity of the
disease, about 0.1 .mu.g/kg to about 0.1 mg/kg to about 50 mg/kg
body weight (e.g., about 0.1-15 mg/kg/dose) of polypeptide can be
an initial candidate dosage for administration to the patient,
whether, for example, by one or more separate administrations, or
by continuous infusion. For example, a dosing regimen may comprise
administering an initial loading dose of about 4 mg/kg, followed by
a weekly maintenance dose of about 2 mg/kg of the polypeptide, or
about half of the loading dose. However, other dosage regimens may
be useful. A typical daily dosage might range from about 0.1
.mu.g/kg to about 1 .mu.g/kg to 100 mg/kg or more, depending on the
factors mentioned above. For repeated administrations over several
days or longer, depending on the condition, the treatment is
sustained until a desired suppression of disease symptoms occurs.
The progress of these and other therapies (e.g., ex vivo therapies)
can be readily monitored by conventional methods and assays and
based on criteria known to the physician or other persons of skill
in the art.
[0383] All publications and patent applications cited in this
specification are herein incorporated by reference as if each
individual publication or patent application were specifically and
individually indicated to be incorporated by reference.
[0384] Although the foregoing invention has been described in some
detail by way of illustration and example for purposes of clarity
of understanding, it will be readily apparent to one of ordinary
skill in the art in light of the teachings of this invention that
certain changes and modifications may be made thereto without
departing from the spirit or scope of the appended claims. The
following examples are provided by way of illustration only and not
by way of limitation. Those of skill in the art will readily
recognize a variety of noncritical parameters that could be changed
or modified to yield essentially similar results.
Example 1
Generation and Characterization of Stable Monomeric and Dimeric
Forms of YRS
[0385] The N-terminal fragment of human tyrosyl-tRNA synthetase,
mini-YRS, is a leukocyte chemo-attractant and an angiogenic factor.
However, the details of how mini-YRS mediates cytokine signaling
are unclear. Mini-YRS exists as both a monomer and a dimer at
physiological conditions. Because mini-YRS mediates cytokine
signaling at a concentration of 10 nM and dimerizes at .gtoreq.100
nM, and because its stimulating effect exhibits a bell-shaped
concentration dependence, it was hypothesized that the monomer form
is the active cytokine and the dimer is a nonfunctional receptor
binding form. To test this hypothesis, a non-associating monomeric
and a non-dissociating dimeric forms of YRS were rationally
designed and characterized, as detailed below.
[0386] The three-dimensional structure of mini-YRS shows that three
residues (Pro 159, Leu 160 and Leu 161) in the CP1 dimerization
domain form backbone H-bonding interactions with the other subunit
(See FIG. 2B), and these three residues were deleted to generate a
stable and substantially monomeric form of YRS.
[0387] To generate a non-dissociating dimer, a disulfide trap
strategy was employed, in which an exposed cysteine residue was
introduced at the dimer interface of each individual monomer so
that the --SH groups are spatially proximal to each other, and upon
oxidation resulted in a single disulfide link across the dimer
interface. As shown in FIG. 2C, Thr 130 was replaced with Cys,
followed by I.sub.2 oxidation to form disulfide bond between two
subunits (named C130.sup.OX).
[0388] Plasmid Construction, Expression, and Purification of
Mini-YRS Variants.
[0389] Plasmid encoding wild-type (WT) human mini-YRS has been
cloned previously, and this plasmid template was used to generate
mini-YRS variants by site-directed mutagenesis using QuikChange.TM.
mutagenesis kit from Stratagene (La Jolla, Calif.). Primers were
purchased from Integrated DNA Technology, Inc. (Coralville, Iowa).
Recombinant proteins were expressed and purified according to
routine techniques in the art. To perform I.sub.2 oxidation, T130C
mini-YRS (1 mg/ml) was incubated with I.sub.2 (0.5 mM) in phosphate
saline buffer (PBS) for 15 min at 37.degree. C., followed by
extensive dialysis overnight against PBS at 37.degree. C. to remove
I.sub.2. Endotoxin was removed by running through EndoTrap Red
column (Lonza Walkersville, Inc., Walkerville, Md.) twice.
[0390] To confirm that the stable monomeric .DELTA.159-161 and
dimeric C130.sup.OX were folded correctly, a circular dichroism
(CD) analysis was performed. Circular dichroism (CD) spectra were
obtained with CD Spectrometer 400 (Biomedical, Inc. Lakewood,
N.J.). Prior to CD measurements, protein samples were extensively
dialyzed overnight against PBS. The measurements were performed
using 100 .mu.L of each protein sample at 10 .mu.M for far-UV
spectra and 500 .mu.L at 50 .mu.M for near-UV spectra. For thermal
melting scans, protein samples were monitored at a fixed wavelength
of 220 nm as a function of temperature.
[0391] These analyses show that the secondary structures of
.DELTA.159-161 and C130.sup.OX are similar to that of the WT (FIG.
3B). Thermal melting also indicates that there is no change in
stability of the .DELTA.159-161 compared to the WT (FIG. 3C).
Near-UV CD spectral region of 260-320 nm arises from aromatic amino
acids, which can be used as a tertiary structure fingerprint. Here,
there is no significant difference in the CD spectra of the WT and
the .DELTA.159-161 except at the region of 275-285 nm (FIG. 3D).
This region corresponds to the signal of tyrosine residues. Based
on the three-dimensional structure, tyrosine residues are the only
aromatic amino acid proximal to the dimer interface, which is
consistent with disruption of dimer interface.
[0392] An amino acid activation assay was then performed to
determine whether the monomeric .DELTA.159-161 and dimeric
C130.sup.OX YRS polypeptides have the ability to aminoacylate their
cognate tRNAs. Homodimerization and half-of-the sites activity of
YRS are required for aminoacylation function. Thus, if any
mutations interfere with the dimerization dynamics they would
likewise affect aminoacylation activity.
[0393] The amino acid activation was performed at 25.degree. C.
according to standard protocols, with some modifications to adapt
to a 96-well format. Briefly, each reaction mixture contained 100
mM Tris-HCl, pH 7.4, 10 mM MgCl.sub.2, 1 mM ATP, 0.1 mg/ml bovine
serum albumin, 0.5 mM sodium pyrophosphate including
[.sup.32P]-pyrophosphate (Perkin Elmer; with specific activity of
37 TBq/mml), 5 mM .beta.-mercaptoethanol, 2 mM tyrosine, and 100 nM
of WT or its variants. Aliquots were quenched at different time
points in 96-well Multiscreen filter plate (Millipore, Billerica,
Mass.) containing 200 mM sodium pyrophosphate, 1 M HCl and 4% (w/v)
activated charcoal. After washing four times with a solution of 200
mM sodium pyrophosphate and 1 M HCl, charcoal-absorbed
[.sup.32P]-ATP samples were punched from the plate and quantified
by scintillation counting. FIG. 3E shows that the .DELTA.159-161
and C130.sup.OX constructs lack aminoacylation activity (FIG.
3E).
[0394] Analytical gel filtration chromatography was then performed
on the stable monomeric .DELTA.159-161 and dimeric C130.sup.OX YRS
polypeptides, in comparison to WT mini-YRS. Each protein sample
(200 .mu.l of 20 .mu.M) was injected to Superdex 200 chromatography
column (GE Healthcare, 10/300GL) in PBS containing 5 mM
.beta.-mercaptoethanol. The column was then calibrated by standard
proteins. These results show that the WT and the C130.sup.OX elute
as dimeric species, whereas the .DELTA.159-161 shifts the
equilibrium distribution toward monomeric species at 10 .mu.M
concentration (FIG. 4A). To determine the dissociation constant for
dimer-monomer equilibrium, gel chromatography was carried out as a
function of protein concentration. As shown in FIG. 4B, the
dissociation constant for .DELTA.159-161 was estimated to be
.about.100 .mu.M. Due to undetectable UV-absorbance at low
concentration of the WT, fractions were collected and
immuno-blotted with a YRS polyclonal antibody. FIG. 4C shows that
at concentrations of 60 nM and 250 nM, WT exists predominantly as
monomers and dimers, respectively. Based on these data, it was
estimated that the dissociation constant for dimer-monomer
equilibrium of WT mini-YRS is .about.100 nM, which is about
1000-fold lower than for the monomeric .DELTA.159-161 YRS
polypeptide.
Example 2
Effects of Stable Monomeric and Dimeric Forms of YRS on
Polymorphonuclear Cell Migration
[0395] To test the hypothesis that the monomer form is the active
cytokine for mini-YRS signaling and that the dimer binds to the
receptor but does not signal, the effect of the monomeric
.DELTA.159-161 and dimeric C130.sup.OX variants on human
polymorphonuclear (PMN) leukocytes was examined. Also, to
understand why the WT min-YRS exhibits a bell-shaped concentration
dependence response but the .DELTA.159-161 does not, competitive
cell migration assays were performed, in which PMN cells were
pre-treated with a progressive increase in either monomer or dimer
concentrations prior to the cell migration assay.
[0396] Transwell Cell Migration Assay.
[0397] Human PMN cells were prepared from heparin-treated whole
blood from healthy volunteers using RosetteSep Human Granulocyte
Enrichment Kit (StemCell Technologies, Vancouver, BC, Canada).
Isolated PMN cells were resuspended in cell migration medium
containing RPMI 1640 (American Type Culture Collection, Manassas,
Va.) and 0.5% heat-inactivated fetal bovine serum (FBS) (Invitrogen
Corporation, Carlsbad, Calif.) and incubated with Calcein AM
(Invitrogen Corporation, Carlsbad, Calif.) at 37.degree. C. in a 5%
CO.sub.2 incubator for 30 minutes. After the incubation, cells were
then collected and washed with RPMI 1640 containing 0.5% FBS two
times and resuspended in cell migration medium at a concentration
of 10.times.10.sup.6 cells/ml.
[0398] Cell migration was performed using 24-well transwell
permeable support with 5 .mu.M pores (Corning Inc., Lowell, Mass.).
Briefly, 100 .mu.L of cells were plated in upper transwell insert
and 600 .mu.L of proteins at various concentrations as labeled in
Figure legends were added to the lower chamber. Cells were allowed
to migrate at 37.degree. C. in a 5% CO.sub.2 incubator for 45
minutes. The migrated cells were then collected and fluorescence
intensity of migrated cells were counted using Synergy HT
Microplate reader with filters set to 485 nm for excitation and 520
nm for emission (BioTek Instruments, Inc, Vinooski, Vt.). Fold
migration over control was calculated as fluorescence intensity of
cells migrating to proteins divided by fluorescence intensity of
cells migrating to medium.
[0399] The results are shown in FIGS. 5 and 6. At low concentration
regime, the monomeric .DELTA.159-161 stimulates PMN cell migration
as effective as the WT (compare FIGS. 5A and B, at 1 nM and 10 nM).
Since the K.sub.d for dimer-monomer equilibrium of WT is .about.100
nM, at this low concentration regime WT exists predominantly as
monomers. In addition, no migration activity was observed in the
treatment with the C130.sup.OX (FIG. 5C). Taken together these
results suggest that the monomer is the active ligand and the dimer
is inactive with respect to inducing PMN migration.
[0400] For the competitive cell migration assays, the dimer
inhibited cell migration in a dose-dependence manner, but the
monomer did not show any inhibition (FIG. 6). These data show that
the dimer is not only the inactive form but also inhibits the
cytokine activity of the monomer.
Example 3
Cytokine Receptor-Binding Characteristics of Stable Monomeric and
Dimeric Forms of YRS
[0401] The monomeric .DELTA.159-161 and dimeric C130.sup.OX YRS
variants were tested for their ability to bind CXCR-1 and CXCR-2 on
the cell surface. Also, competitive binding assays were performed
in the presence of fixed concentration of WT min-YRS and increasing
concentration of dimer to determine whether the dimer competes with
WT mini-YRS for binding to the receptor. In these assays, HEK 293
cells that stably express either CXCR1 or CXCR2 receptors were
incubated with purified His.sub.6-tagged WT mini-YRS, monomeric
.DELTA.159-161 mini-YRS, or the C130.sup.OX dimeric variant.
[0402] Receptor Binding Assay.
[0403] HEK 193 cells that express CXCR-1 or CXCR-2 (a gift from Dr.
Adit Ben-Baruch at Tel Aviv University) were incubated with
purified His.sub.6-tagged WT or .DELTA.159-161 mini-YRS for 1 hr at
4.degree. C. Cells were then washed twice with PBS, lysed with
M-PER buffer (Thermo Scientific, Rockford, Ill.) and analyzed by
immunoblotting using anti-His.sub.6 (Immunology Consultants
Laboratory, Inc. Newberg, Oreg.) and anti-actin (Sigma-Aldrich, St.
Louis, Mo.) antibodies to detect mini-YRS binding and relative
number of cells, respectively. The expression of CXCR-1 or CXCR-2
in these cells was confirmed by flow cytometric analysis (data not
shown).
[0404] These results are shown in FIGS. 7 and 8. As shown in FIG.
7, the monomer binds to cells expressing the CXCR-1 and CXCR-2
receptors as effective as the WT. In addition, no binding was
observed to the non-receptor-expressing parental HEK 293 cell line.
As shown in FIG. 8, increasing concentration of the C130.sup.OX
dimer results in decrease in binding of the WT mini-YRS.
[0405] The results herein show that the dissociated monomer is
functionally active and the dimer is not active. Moreover, the
dimer functions as an antagonist by competing with the monomer for
receptor binding, resulting in shutting down the monomer-induced
cytokine activity. This work provides a new mechanism for
understanding how new surfaces can be exploited to expand new
functions of tRNA synthetase.
Example 4
VE-Cadherin Interacts with Monomeric Form of T2-WRS
[0406] To test the nature of the interaction between human
tryptophanyl tRNA synthetase and the extracellular domain EC1 of
VE-cadherin, the T2-WRS fragment of WRS and the EC1 domain of
VE-cadherin were recombinantly expressed and purified. These
purified polypeptides were then mixed together, and separated by
size exclusion chromatography, as detailed below.
[0407] Expression and Purification of Recombinant T2-WRS.
[0408] Human T2-WRS cDNA (residues 94-471 of full-length WRS) with
a C-terminal His6 tag was cloned into plasmid pET20b. T2-WRS was
expressed in E. coli strain BL21 (DE3) (Novagen) by induction for 4
hr with 1 mM isopropyl .beta.-D-thiogalactopyranoside. Protein was
purified from the supernatants of lysed cells using Ni-NTA agarose
column chromatography (Qiagen) according to the manufacturer's
instruction.
[0409] Expression and Purification of VE-Cadherin Extracellular
Domain EC1.
[0410] VE-Cadherin extracellular domain EC1 (residues 48-155 of
full-length VE-Cadherin) was cloned into pGEX-6p-1 (GE Healthcare)
vector with a glutathione transferase (GST) tag at its N-terminal,
and the resulting plasmid was transformed into Escherichia coli
BL21(DE3) cells. The recombinant GST fusion protein, GST-VE-EC1,
was purified by GST-glutathione affinity chromatography. A Factor
Xa recognition sequence Ile-Glu-Gly-Arg was cloned between the
first residue of VE-EC1 and the GST tag to allow the cleavage of
GST tag from VE-EC1. The Factor Xa cleavage reaction was performed
at 4.degree. C. for 20 hours in a buffer containing 25 mM Tris
pH8.0, 100 mM NaCl and 2 mM CaCl.sub.2. The tag-free VE-EC1 was
then purified by gel filtration chromatography (Superdex200 HR
10/30, GE Healthcare) in a buffer containing 25 mM Tris-HCl (pH
8.0), 150 mM NaCl.
[0411] To perform the size exclusion chromatography experiment,
T2-WRS and VE-EC1 were loaded separately or together at a molar
ratio of 1:1 on Superdex 200 HR 10/30 column, and then eluted at
0.5 mL min with a buffer containing 25 mM Tris-HCl (pH 8.0), 150 mM
NaCl. The results are shown in FIG. 10; FIG. 10A shows the results
for T2-WRS, FIG. 10B shows the results for VE-Cadherin EC1 domain,
FIG. 10C shows the results for T2-WRS and VE-EC1 at 1:1 ratio with
0.1 mM Zn.sup.2+, and FIG. 10D shows the results for T2-WRS and
VE-EC1 at 1:1 ratio with 0.1 mM Zn.sup.2+ and 30 uM Trp-SA. These
results illustrate the selective association of the EC1 domain of
VE-cadherin with monomeric forms of WRS.
Example 5
Generation and Characterization of WRS Variants that Form Stable
Monomers
[0412] To construct monomeric forms of WRS, the 3D structure of
T2-WRS was first analyzed to identify potentially relevant residues
(e.g., F260, Y201 and I278) in the dimer interface, and also to
identify alternate residues of potential relevance (e.g., H130 and
E408). See FIG. 11. Certain residues were then selected for point
mutation, to generate the exemplary F260EY201EI278E (SEQ ID NO:8)
and F260EY201EH130R (SEQ ID NO:9) variants of T2-WRS.
[0413] T2-WRS variants were constructed by QuikChange Site-Directed
Mutagenesis Kit (Stratagene). The point mutations were confirmed by
DNA sequencing. Plasmid contains specific mutational amino acids
was transformed to E. coli BL21(DE3) for protein expression. The
variants F260EY201EI278E and F260EY201EH130R were induced at room
temperature for 4 hours with 0.2 mM isopropyl
.beta.-D-thiogalactopyranoside, and were purified by Ni-NTA
affinity chromatography. The elutes were further purified by
ion-exchange chromatography (MonoQ HR5/5, GE Healthcare), and
eluted at 0.5 mL min.sup.-1 with a buffer containing 25 mM Tris-HCl
(pH 8.0) and gradient concentration of NaCl.
[0414] The oligomeric or monomeric state of the variant proteins
was then verified by gel filtration chromatography (Superdex200 HR
10/30, GE Healthcare) in a buffer containing 25 mM Tris-HCl (pH
8.0), 150 mM NaCl. Specifically, as shown in FIG. 11, WT T2-WRS
(FIG. 11A), F260EY201EI278E T2-WRS (FIG. 11B) and F260EY201EH130R
T2-WRS (FIG. 11C) were loaded on Superdex200 HR 10/30 column and
eluted at 0.5 mL min.sup.-1 with a buffer containing 25 mM Tris-HCl
(pH 8.0), 150 mM NaCl. This size exclusion chromatography analysis
confirms that T2-WRS variants F260EY201EI278E and F260EY201EH130R
exist as monomers in solution.
[0415] Size exclusion chromatography was then used to determine the
dimer-monomer dissociation constant of T2-WRS. T2-WRS was loaded on
Superdex 200 HR 10/30 column and eluted at 0.5 mL min.sup.-1 with a
buffer containing 25 mM Tris-HCl (pH 8.0), 150 mM NaCl. The
concentration of T2-WRS was from 100 nM to 10 uM (see FIG. 14A). As
shown in FIG. 14B, the percentage of dimers was calculated and
plotted as a function of the protein concentration to determine the
dimer-monomer dissociation constant (K.sub.d=0.437.+-.0.03 .mu.M).
Similar experiments were performed for the T2-WRS\
(F260EY201EI278E) monomer; however, the K.sub.d for the monomeric
form was not able to be accurately determined by this method. Even
at the highest concentration prepared (.about.270 .mu.M), the
protein was still predominately in monomeric conformation. The
K.sub.d for T2-WRS\ (F260EY201EI278E) was thus estimated to be
greater than 1 mM.
Example 6
WRS Monomers Interact with VE-EC1 and Induce Degradation of
B-Catenin
[0416] Immunoprecipitation experiments were performed to
characterize the interaction of WRS monomers with the extracellular
domain EC1 of VE-cadherin. Briefly, VE-EC1 was biotinylated and
incubated with Strep-Tactin beads as bait. After incubation with
T2-WRS and its variants (100 nM), the beads were washed three times
and the bound T2-WRS and its variants were detected by
anti-6.times.His antibody by Western blotting. To investigate the
Zn2+ dependence of the interaction, ZnCl.sub.2 (10 uM) or Zinc
chelator 1,10-phenanthroline (1 uM) were added in the assay.
[0417] Preparation of Biotinylated VE-EC1.
[0418] VE-EC1 was constructed with a Cysteine at its C-terminal,
and then the engineered protein was purified and biotinylated using
Maleimide-PEG2-Biotin (Thermo Scientific), which contains a spacer
arm of 29.1 .ANG..
[0419] Immunoprecipitation Assay.
[0420] VE-EC1-biotin was immobilized to Strep-Tactin beads as bait
to pull down T2-WRS and its variants F260EY201EI278E and
F260EY201EH130. VE-EC1-biotin and T2-WRS and its variants were
incubated in a buffer containing 25 mM Tris-Cl pH8.0, 150 mM NaCl
and 0.1% Triton X-100 for 1 hours at 4.degree. C., then it was
centrifuged and washed by binding buffer three times, and the bound
protein was then washed with 30 .mu.l of reduced slab gel sample
buffer (final 5% SDS, 5 mM .beta.-ME) and the sample was heated at
95.degree. C. for 5 min and centrifuged at 10,000 rpm for 10 min,
the supernatant was resolved by 4-20% gradient Tris-glycine
SDS-PAGE and transferred to a nitrocellulose membrane.
[0421] Western Blotting.
[0422] After blocking with 5% milk-TBS-TW20, immunoblotting was
performed using HRP conjugated rabbit anti-6.times.His antibody
(Immuno Consultants Laboratory) human WRS or goat anti-human IgG-Fc
antibody (Jackson Immuno Research), and with SuperSignal
chemiluminescence substrate (Thermo Scientific). The bands were
visualized by x-ray autoradiography.
[0423] The results are shown in FIG. 12. As indicated in this
Figure, the T2-WRS variants F260EY201EI278E T2-WRS and
F260EY201EH130R T2-WRS bind strongly to VE-EC1 under a variety of
conditions, and in the absence of zinc bind stronger to VE-EC1 than
T2-WRS.
[0424] Biacore Analysis.
[0425] Surface plasmon resonance analysis (Biacore) was then used
to measure and compare the interaction between the VE-Cadherin EC1
domain and two different T2-WRS\ polypeptides (wild-type T2-TprRS;
and the monomer F260EY201EI278E T2-WRS). Each T2-WRS polypeptide
was separately immobilized to a CM5 sensor chip by direct amine
coupling through the side chain of Lys residues. Recombinantly
engineered VE-Cadherin EC1 domain was then allowed to flow through
the surface of the chip at different concentration series in buffer
containing 10 mM Hepes pH7.5, 150 mM NaCl, 0.1 mM ZnCl.sub.2, and
0.005% surfactant P-20. As shown in FIGS. 15A and 15B, the
dissociation constant was measured by kinetic titration fitting as
1.52 .mu.M for WT T2-WRS (15A) and 1.34 .mu.M for the monomer
T2-WRS (15B). The relatively low binding between T2-WRS and EC1
suggests that domains outside EC1 may also contribute to binding of
T2-WRS. Nevertheless, the monomer T2-WRS binds to EC1 domain as
tight as the WT protein, if not tighter.
[0426] WT T2-WRS and monomer T2-WRS also induce degradation of
.beta.-catenin. Because .beta.-catenin is one of the intracellular
association factors of VE-Cadherin, and dissociated .beta.-catenin
is degraded by the proteosome (see FIG. 16A), tests were then
performed to determine whether binding of T2-WRS polypeptides would
disassociate .beta.-catenin from VE-Cadherin and lead to its
degradation. As shown in FIG. 16B, treatment of VE-Cadherin
expressing C8161 melanoma cells with 1 .mu.M of either WT T2-WRS or
monomer T2-WRS (F260EY201EI278E) caused a sharp decrease in
.beta.-catenin protein levels.
[0427] To confirm that F260EY201EI278E T2-WRS retains its monomeric
form at higher concentrations (e.g., above 1 .mu.M), such as those
used in the .beta.-catenin experiment described above, WT and
F260EY201EI278E T2-TrpRS were loaded on a Superdex 200 HR 10/30
column and eluted at 0.5 mL min with a buffer containing 25 mM
Tris-HCl (pH 8.0), 150 mM NaCl. Concentrations of WT and monomeric
T2-TrpRS were 100 .mu.M and 270 .mu.M. FIG. 16C shows that even at
270 .mu.M, F260EY201EI278E T2-TrpRS is still predominately in
monomeric conformation. The estimated dimer-monomer dissociation
constant (Kd) for F260EY201EI278E T2-TrpRS is greater than 1
mM.
Example 7
WRS Monomers Reduce Angiogenesis
[0428] To test the angiogenic-modulating activity of WRS monomers,
an endothelial cell tuber formation assay was performed.
Endothelial cell line (3B11, ATCC) was maintained in RPMI 1640
medium (Invitrogen) supplemented with 10% FBS (Invitrogen) and
1.times. solution of penicillin and streptomycin in an atmosphere
of 5% CO.sub.2 in air at 37.degree. C. Two days before performing
the tube formation assay, 6.times.10.sup.5 3B11 cells were cultured
in a T75 flask. The cells reached 80 to 95% confluence on the day
of the tube formation assay.
[0429] The assay was performed as previously described (see, e.g.,
Zhou et al., 2008). Briefly, 150 .mu.l of matrigel was transferred
to 48-well plates and incubated for 30 min at 37.degree. C. in an
atmosphere of 5% CO.sub.2. 100 .mu.l of purified T2-WRS or other
testing agents were mixed with 100 .mu.l endothelial cells
(4.times.10.sup.5/ml in RPMI 1640 complete medium), and the mixture
(200 .mu.l) was transferred to each well containing the matrigel
matrix. The plates were incubated at 37.degree. C., 5% CO.sub.2 for
3-8 h. The cells were imaged with a Leica DC350F CCD camera
attached to an inverted Leica DMIL microscope, and then captured
using ProMax software (Bio-TEC Instruments). Images were then
converted to high resolution tif files that were used for
analysis.
[0430] The results for T2-WRS, F260EY201EI278E T2-WRS, and
F260EY201EH130R T2-WRS are shown in FIG. 13. These images
illustrate that the engineered T2-WRS monomers are active in
inhibiting angiogenesis.
[0431] As shown in FIG. 17, an additional tuber formation assay was
performed to demonstrate that the most potent angiostatic activity
of WT T2-TrpRS is at 50 nM, a concentration at which WT T2-TrpRS
has a predominately monomer conformation according to its
dimer-monomer dissociation constant of 472 nM. For each experiment,
multiple repetitions were performed. The length (mm) of the
connected vessels in each experiment was calculated and the average
length+/-SEM (standard error of the mean) for each group is shown
side-by-side with a representative image.
Example 8
Generation and Characterization of Lysyl-tRNA Synthetase (KRS)
Variants that Form Stable Monomers
[0432] The interactions between KRS (also LysRS), HIV Gag, and
tRNA.sup.Lys were explored by modeling to help design and determine
the characteristics of monomeric versions of KRS. First, ab initio
computational methods together with high resolution 3-D structure
of human KRS produced an energy-minimized docking model where Gag,
tRNA.sup.Lys, and KRS form a ternary complex. Interestingly, the
model required otherwise homodimeric KRS to dissociate into a
monomer that bridges between Gag and tRNA.sup.Lys3--in part because
the KRS-Gag interface was seen to overlap the covered surface of
the .alpha..sub.2 KRS dimer interface. This result raised the
possibility that the dynamic equilibrium of KRS between monomer and
dimer states could direct the protein from aminoacylation (which
requires the dimer) to HIV packaging (monomer, which is inactive
for aminoacylation).
[0433] Docking Model.
[0434] Briefly, coordinates of Gag-CA-CTD were taken from the
crystal structure of CTD (pdb ID: 1A8O). Initial docking of CTD on
both monomer and dimer structures of human KRS (pdb3BJU) was
estimated using ZDOCK. The solutions were clustered by ClusPro with
binding energies calculated by both FastContact and Dcomplex. Then
a blind-docking of CTD on the monomer structure of human KRS was
performed with the default parameter on 3 docking programs, HEX,
ZDOCK and Dot..sup.12-14 The binding site was screened by docking
the CA-CTD domain on all surfaces of the human KRS structure
(pdb3BJU, chain A). Next, the docking of the CA-CTD domain was
refined in a 50-.ANG. size cubic space centering on the dimer
interface. A thorough rigid-body docking was carried out using
AutoDock. After searching with the maximum grids and clustering,
the large cluster with the lowest energy showed apparent separation
from all the others. Then, this lowest energy solution was
subjected to molecular dynamic refinement in four steps by CNS:
rigid-body torsion angle dynamics of two groups (KRS and CA-CTD,
500 MD cooling steps from 2000 K with a 8 fs time step), rigid-body
torsion angle dynamics of three groups (KRS_N, KRS_C and CA-CTD,
500 MD steps from 2000K), semi-flexible simulated annealing (1000
MD steps from 1000 K with 4 fs time steps) with side chains of the
interface residues, and a final semi-flexible simulated annealing
(1000 MD steps from 1000K to 50K with 2 fs time steps), where both
side chains and backbones of the interface residues were allowed to
move to allow for conformational arrangement. After the MD
refinement, the interaction energy (sum of E.sub.elec, E.sub.vdw,
E.sub.ACS) decreased from -10691.001 to -11788.829 kcal/mol.
[0435] Results.
[0436] Using Zdock, as noted above, a systematic rigid-body docking
of Gag-CA-CTD was performed with both the monomer and, separately,
the dimeric structure of human KRS. In the top 10 clusters of CTD
dockings to dimeric KRS, nine showed CTD binding to only one
subunit of dimeric KRS. For one cluster, CTD bound to both subunits
of dimeric KRS, but with only about half the binding energy
compared to the other top hits. Thus, binding of CTD of the two
subunits of dimeric KRS is unfavorable. When CTD was docked on the
monomeric structure of human KRS, the docking sites were localized
predominantly to the exposed residues used to form the dimer
interface. This interface is covered and, therefore, inaccessible
in dimeric KRS. Thus, the congruence of the primary docking trial
suggested CTD has a tendency to bind to monomeric human KRS.
[0437] To confirm this result, a few well-developed computational
docking programs were tested to achieve an unbiased fit of
monomeric KRS with Gag-CA-CTD. Complete searches of all
orientations between the two proteins were done by systematically
rotating and translating a moving Gag-CA-CTD with a stationary KRS.
Interaction energies were computed as the sum of van der Waals and
electrostatic terms (see Methods). Significantly, docking
Gag-CA-CTD to monomeric human KRS by each of 3 programs (HEX,
Zdock, Dot) identified one common Gag-CA-CTD binding site. As shown
in FIG. 18A, this common site fell within 90-95% of the solutions
represented in the 200 top-ranked solutions for all 3 programs. For
this common docking site, Gag-CA-CTD docking solutions were located
in a 35-.ANG. wide cavity of KRS formed by the N-terminal
anticodon-binding domain and the C-terminal aminoacylation domain.
This cavity is a major part of the surface needed to form the KRS
homodimer, and constitutes .about.60% of the entire dimeric
interface between individual KRS monomers. The bottom of this
cavity forms the largest hydrophobic patch of the KRS surface. The
extensive overlap of these docking solutions from independent
docking algorithms strongly suggests that this cavity is the
preferred site for binding of KRS to Gag-CA-CTD.
[0438] To enumerate all possible binding orientations, Autodock was
then utilized as above to enumerate all possible binding
orientations, a technique that can be used for accurate placement
of small molecules on proteins. This second step `Autodock
analysis` was performed in a defined cubic space (50 .ANG..times.50
.ANG..times.50 .ANG.) centered on the inter-domain cavity (formed
between aminoacylation and anticodon-binding domains) that was seen
in the profile of the initial general searches (see FIG. 18B).
Significantly, Autodock gave a cluster of docking orientations
having the lowest energy, and well separated from other clusters.
The largest grouping is the 2.sup.nd lowest energy cluster, located
within a broad but shallow energy state. In contrast, the lowest
energy cluster sits in a deep but narrow energy funnel. Thus, a
specific orientation of the two molecules defines the lowest energy
interaction.
[0439] Model of Human KRS/tRNA.sup.Lys3/Gag-CA Ternary Complex.
[0440] With the KRS/CA-CTD docking model as a reference, a model of
the tRNA.sup.Lys3/KRS/Gag-CA-CTD complex was constructed. This
process utilized structural information on E. coli AspRS in complex
with tRNA.sup.Asp (KRS is more closely related to AspRS than to any
other tRNA synthetase). The tRNA from the E. coli
AspRS-tRNA.sup.Asp complex structure (pdb1ASY) was built onto human
KRS by simple superposition of the respective catalytic domains
(see FIG. 19). To complete the full structure of human KRS, the
N-terminal eukaryotic extension was added--this structure is
thought to bind nonspecifically to the acceptor-T.psi.C stem-loop
domain of tRNA. The N-terminal portion of the extension is
predicted as a long helix that is positioned on the elbow region of
the modeled tRNA This positioning utilized the functionally similar
A1 domain of Thermus thermophilus PheRS bound to tRNAPhe (pdb1EIY).
This strongly dipolar lysine-rich helix has a positive
electrostatic potential extending out from one side of the protein
to form part of the RNA-binding site. The N-terminal domain (NTD)
of the capsid protein was then manually docked onto the complex by
superimposing Gag-CA-CTD from the known structure of the Fab-capsid
complex (pdb1E6J). Although the linker between N- and C-domains of
the capsid protein is flexible, and the capsid protein can adopt
multiple conformations that are important for virion assembly,
Gag-CA-CTD was positioned far from tRNA.sup.Lys in the
KRS-tRNA.sup.Lys3 complex--a position with least impact on the
binding interface (see FIG. 19). Here, the C-terminal end of CTD
(shown as lower arrow in FIG. 19) points to tRNA.sup.Lys in the
modeled complex, thus allowing the C-terminal nucleocapsid part of
Gag to easily access the packaged tRNA. This model suggests that
Gag-CA-CTD alone is sufficient to bind to KRS, and that the rest of
Gag is dispensable for binding to KRS.
[0441] Because the KRS/Gag-CA-CTD interface overlaps with the core
of the KRS homodimer interface, a monomer form of KRS is required
to access that interface. Given that dimeric KRS and the modeled
KRS/Gag-CA-CTD complex share the interface, a stabilized monomer
form of KRS was designed and tested to see if its potential Gag
binding interface remaining intact, and to measure its capacity for
binding tRNA.sup.Lys3. One goal was to disrupt the KRS dimer
interface without affecting the interface of KRS with
Gag-CA-CTD.
[0442] One approach utilized a large globular insertion (at least
about 30 .ANG. in diameter) on the periphery of the dimer
interface, to provide enough steric hindrance to block dimer
formation. The following criteria were preferred: (i) the
insertional sequence is not a membrane protein (so as to not
introduce an extra hydrophobic surface for protein-protein
interactions), (ii) it has a globular 3D structure, (iii) having
about 30-40 .ANG. dimension, and (iv) its N-terminus and C-terminus
are located in close proximity, for instance, to minimize a
structural change when inserted it into a single site. The
structure of E. coli Flavodoxin (pdb1ahn) is one example of an
insertion that satisfies all of these criteria. As briefly
described below, the gene encoding this .about.180 amino acid
protein was then amplified, cloned and inserted at the G310
position of human KRS (see FIG. 20C). The resulting recombinant
Flavo-KRS fusion protein was expressed and purified.
[0443] Constructs and Protein Expression.
[0444] All constructs were generated using a standard polymerase
chain reaction-based cloning strategy. Full length KRS (1-597) and
its truncated form (70-584) were expressed in the bacterial strain
BL21 (DE3) CodonPlus using the pET20b vector (Novagen). Both
proteins contained a C-terminal 6.times.His tag, and were purified
to homogeneity by a Ni-NTA affinity column (Qiagen, Valencia,
Calif.) and a Q high performance column (GE Healthcare, Little
Chalfont, Buckinghamsire, U.K.). All proteins were concentrated in
5 mM Tris-HCl buffer, pH 8.0, 50 mM NaCl and 5 mM
beta-mercaptoethanol.
[0445] Engineering of KRS.
[0446] Mutations on the truncated form of human KRS (70-584) were
introduced by the QuikChange Mutagenesis PCR method (Stratagene)
and verified by DNA sequencing. The E. coli fldB gene encoding
Flavodoxin-2 (UniprotKB: P0ABY4) was amplified from E. coli K-12
genome DNA. It was then inserted into either empty pET20b vector,
or into the human KRS expression plasmid using the QuikChange
method modified for large insertions. All proteins were expressed
and purified identically to native human KRS.
[0447] Gel Filtration Chromatography.
[0448] For each assay, 500 .mu.l of purified truncated human KRS
(70-584) and its mutants were applied to a Superdex 200
chromatography column (GE Healthcare, 10/300 GL) in a buffer
containing 25 mM HEPES, pH7.5, 150 mM NaCl and 5 mM
beta-mercaptoethanol. The peak fractions were analyzed by SDS-PAGE
and visualized by Coomassie blue staining.
[0449] Crosslinking Assay.
[0450] A T285C mutation was introduced into native human KRS
(70-584) and Flavo-KRS (70-584). All proteins were expressed and
purified as mentioned above, except that no beta-mercaptoethanol
was added. The purified proteins were diluted to 1 mg/ml in 25 mM
HEPES (pH7.5, 150 mM NaCl) and incubated for 15 minutes at
4.degree. C. with or without 10 mM DTT (dithiothreitol). Proteins
samples (10 .mu.l) were mixed with an equal amount of 2.times.
loading buffer (without reducing reagent) and boiled for 1 min
before loading onto a SDS-PAGE gel.
[0451] Gel filtration, at a loading concentration of 2 .mu.M,
showed that Flavo-KRS ran mostly as a monomer (see FIG. 20D). FMN
(flavin mononucleotide) bound to native E. coli flavodoxin has a
characteristic absorbance centered at 466 nm, thus giving a bright
yellow color. Purified Flavo-KRS had a similar absorbance spectrum,
consistent with the flavodoxin domain of the fusion protein being
in the native conformation (see FIG. 21A).
[0452] To verify the monomeric state of Flavo-KRS seen by gel
filtration, the above-noted crosslinking assay was then carried out
in solution. For this purpose, it was noted that two
.beta.-hairpins in the aminoacylation domain of each monomer form
an anti-parallel hydrogen bonded .beta.-sheet interaction, as part
of the dimer interface. The Thr285 side chains of these hairpins on
the two subunits are 4.5 .ANG. apart (see FIG. 21B). Because this
spacing could accommodate a disulfide crosslink, a T285C mutation
was introduced into both native- and Flavo-KRS. With this T285C
substitution, native KRST285C spontaneously formed a covalent dimer
during purification; in contrast, native KRS did not. Addition of 5
mM dithiothreitol (DTT) converted the covalent dimer into a monomer
on the SDS-PAGE gel (see FIG. 21B). In contrast, for WT and T285C
Flavo-KRS, both forms showed the same pattern, with little
crosslinked dimer found on the SDS-PAGE gel (see FIG. 21B). Thus,
the flavodoxin insertion efficiently disrupted the tight
dimerization of KRS.
Example 9
Monomeric Lysyl-tRNA Synthetase (KRS) Retains HIV Gag and
tRNA.sup.Lys3 Binding
[0453] Based on the KRS/tRNA.sup.Lys/Gag-CA model, the flavodoxin
was designed to insert at a site with KRS that would minimize
steric interference and thus allow complex formation. To confirm
this model, the binding of Flavo-KRS to Gag was experimentally
examined. As described below, and illustrated in FIG. 22A, a
Gag.DELTA.p6 construct fused with the StrepII-tag and bound to
Strep-Tactin beads was used bait in a pull-down assay to measure
monomeric KRS binding to Gag.
[0454] Pull-Down Assay.
[0455] The region 1-448 of Gag.DELTA.p6 (encodes matrix, capsid and
nucleocapsid) was subcloned into a home-made GST fusion vector,
pHisGSTtev. An octapeptide StrepII-tag (sequence WSHPQFEK) was
inserted at the N-terminus of Gag.DELTA.p6. The
HisGSTtev-StrepII-Gag.DELTA.p6 fusion protein was expressed and
purified identically to the procedure used for human KRS. The
N-terminal HisGST was cleaved by TEV protease (1:100) at 4.degree.
C. overnight and removed by passing through a Ni-NTA affinity
column. The purified StrepII-Gag.DELTA.p6 protein was bound onto 50
.mu.l Strep-Tactin beads (IBA, Germany) and washed. Then 200 .mu.l
of 20 .mu.M WT KRS, Flavo-KRS or E. coli Flavodoxin was added to
the beads and incubated at 4.degree. C. for 2 hours. Unbound
proteins were washed with standard washing buffer (100 mM Tris-HCl
(pH8.0), 150 mM NaCl, 1 mM EDTA). Bound proteins were then eluted
with elution buffer (2.5 mM desthiobiotin in washing buffer). The
samples were checked by Western blot using anti-His antibody.
[0456] As shown in FIG. 22B, monomeric Flavo-KRS bound to Gag,
while flavodoxin alone showed no binding to Gag. In this study,
Flavo-KRS also appeared to bind to Gag better than KRS.
[0457] Because packaging in vivo of tRNA.sup.Lys3 into the HIV
virion requires KRS, electrophoretic mobility shift assay (EMSA)
was then performed to investigate binding of tRNA.sup.Lys3 to KRS.
Human tRNA.sup.Lys3 was prepared by in vitro transcription based on
previously described methods. The annealed human tRNA.sup.Lys3 was
then radiolabeled with .sup.32P at the 3'-end. For each complex
formation reaction, about 10,000 cpm of tRNA (diluted with cold
tRNA.sup.Lys3 to a final concentration of 0.1 .mu.M) was incubated
for 10 min on ice with variable concentrations of human KRS or
Flavo-KRS (full-length, 1-597) in a total volume of 20 .mu.l
containing 20 mM HEPES (pH 7.5), 20 mM KCl, 5 mM MgCl2, and 2 mM
DTT. Glycerol was added to a final concentration of 5% in each
sample prior to loading on a native 6% 29:1 polyacrylamide gel. The
gel ran at 100 V for 1.5 hr at 4.degree. C. in 0.5.times.TBE, was
fixed by 7% HOAC for 5 min at 4.degree. C., and then dried onto
analytical filter paper.
[0458] Using the EMSA method, as shown in FIGS. 22B-D, both native
(22B)--and Flavo-KRS (22C) bound tRNA.sup.Lys3 with similar
affinities. FIG. 22D shows that Flavo-KRS had a slightly weaker
affinity of 1.21 .mu.M relative to native KRS (0.87 .mu.M).
Monomeric Flavo-KRS thus retains the ability to bind
tRNA.sup.Lys3.
[0459] Discussion.
[0460] Here, with only structural information, a three-stage
approach was used to predict the binding of human KRS with
Gag-CA-CTD (see FIG. 18). Based on the predominance of both energy
and cluster populations, each program (HEX, Zdock, Dot) yielded
binding sites around the dimer interface of KRS. Thus, the
inter-domain cavity, which is exposed in monomeric KRS, forms a
natural binding site for Gag-CA-CTD.
[0461] The refined docking model also predicted that H3, H4 and the
C-loop of CA-CTD form the binding interface. Consistent with this
prediction, in vitro immunoprecipitation experiments have shown
that removal of H4 (205-231) abolished the ability of CA-CTD to
bind to KRS. In addition, immunoprecipitation assays with whole
cell lysates showed that, without the C-terminal half of CA-CTD
(191-231) that spans the C-loop, the partially deleted Gag loses
its interaction with endogenous KRS. Further dissection showed a
peptide constituting H4 and the C-terminal loop (211-227) in CA can
bind to KRS with an affinity similar to that of CA-CTD. In the
present model, the C-terminal half of the CA-CTD domain, consisting
of helices H3 (196-205) and H4 (211-218), was positioned into the
deeper part of the KRS inter-domain cavity (see FIG. 18E); upon
addition of the C-terminal loop (220-231) of CA-CTD into the
docking model, potential contacts were observed between this loop
and KRS (see FIG. 19). These predicted contacts might explain why
the loop residues were previously shown to give the strongest
shifts in an NMR titration of KRSs with CA-CTD.
[0462] The present docking model also showed that the minimal
CA-CTD binding site is located within a segment at the N-terminal
side of motif 1 (228-255) of KRS (see FIGS. 18C-E). In vitro assays
of others showed that residues 1-308 and 220-597 of KRS each bind
to Gag-CA-CTD with an affinity similar to that of full-length KRS.
Further, in vivo packaging assays also showed that residues 1-259
and 208-597 can be efficiently incorporated into Gag-containing
viral-like-particles. Collectively, these experimental assays
mapped out the minimal binding region of KRS to residues 220-259.
This minimal binding region fits well with the predicted binding
site of 228-255 (see FIG. 18E).
[0463] Based on the present docking model, the full-length
KRS/tRNA/Gag-CA complex has the C-terminal end of the Gag protein
located on the same side as bound tRNA on KRS. In contrast, the
N-terminal end of Gag is on the opposite side. This orientation
would make the packaged tRNA easy to be accessed by the C-terminal
nucleocapsid part of Gag, and GagPol, for productive packaging of
tRNA.sup.Lys3 and annealing to the HIV genome.
[0464] These docking results also showed that H3 and H4 of CA-CTD
bind to the inter-domain cavity of the KRS monomer (see FIG. 18E).
It has been suggested that the available interaction sites on
CA-CTD are limited, with only one site being suitable as a target
for effective inhibitor binding. A 12mer peptide was reported to
bind to a groove spanning H1, H2 and the top of H3 and H4. However,
the present model indicates that the bottom side of H3 and H4 could
form an interaction interface with human KRS and thus represent a
drug target. Because H3, H4 and the C-terminal loop of CA-CTD are
critical for HIV virion assembly, an inhibitor covering the `bottom
side` of H3 and H4 may not only inhibit KRS binding and
tRNA.sup.Lys incorporation, but also effectively block virion
assembly. This model of the complex suggests that binding of KRS
could potentially block efficient dimerization of the CA-CTD
domain; a consideration that suggests KRS-bound Gag may be present
in a different polymeric state compared to other Gag molecules in
the virion.
[0465] Although monomeric KRS is inactive for aminoacylation, these
results showed that disruption of KRS dimerization seems not to
have a major affect on tRNA binding. The N-terminal helix motif
specific to eukaryotic KRS plays a critical role for capturing
tRNA.sup.Lys and contributes significantly to the binding. On the
other hand, based on the crystal structure of the bacterial
KRS-tRNA.sup.Lys complex, tRNA.sup.Lys is mainly anchored through
the interaction of the anticodon stem-loop with the
anticodon-binding domain, with minimal interaction being seen with
the catalytic domain of the synthetase. Because tRNA binding
affinity of monomeric Flavo-KRS is close to that of the native
dimeric KRS, monomeric KRS can efficiently capture tRNA. Other
interactions between tRNA.sup.Lys3 with Gag-Pol may further
stabilize the ternary complex. Thus, among other uses, the
monomeric Flavo-KRS described herein could be a valuable tool for
studying the mechanism of tRNA.sup.Lys3 incorporation into the HIV
virion.
[0466] As noted, the disclosure above is descriptive, illustrative
and exemplary and is not to be taken as limiting the scope defined
by the appended claims which follow.
Sequence CWU 1
1
141528PRTHomo sapiens 1Met Gly Asp Ala Pro Ser Pro Glu Glu Lys Leu
His Leu Ile Thr Arg1 5 10 15 Asn Leu Gln Glu Val Leu Gly Glu Glu
Lys Leu Lys Glu Ile Leu Lys 20 25 30 Glu Arg Glu Leu Lys Ile Tyr
Trp Gly Thr Ala Thr Thr Gly Lys Pro 35 40 45 His Val Ala Tyr Phe
Val Pro Met Ser Lys Ile Ala Asp Phe Leu Lys 50 55 60 Ala Gly Cys
Glu Val Thr Ile Leu Phe Ala Asp Leu His Ala Tyr Leu65 70 75 80 Asp
Asn Met Lys Ala Pro Trp Glu Leu Leu Glu Leu Arg Val Ser Tyr 85 90
95 Tyr Glu Asn Val Ile Lys Ala Met Leu Glu Ser Ile Gly Val Pro Leu
100 105 110 Glu Lys Leu Lys Phe Ile Lys Gly Thr Asp Tyr Gln Leu Ser
Lys Glu 115 120 125 Tyr Thr Leu Asp Val Tyr Arg Leu Ser Ser Val Val
Thr Gln His Asp 130 135 140 Ser Lys Lys Ala Gly Ala Glu Val Val Lys
Gln Val Glu His Pro Leu145 150 155 160 Leu Ser Gly Leu Leu Tyr Pro
Gly Leu Gln Ala Leu Asp Glu Glu Tyr 165 170 175 Leu Lys Val Asp Ala
Gln Phe Gly Gly Ile Asp Gln Arg Lys Ile Phe 180 185 190 Thr Phe Ala
Glu Lys Tyr Leu Pro Ala Leu Gly Tyr Ser Lys Arg Val 195 200 205 His
Leu Met Asn Pro Met Val Pro Gly Leu Thr Gly Ser Lys Met Ser 210 215
220 Ser Ser Glu Glu Glu Ser Lys Ile Asp Leu Leu Asp Arg Lys Glu
Asp225 230 235 240 Val Lys Lys Lys Leu Lys Lys Ala Phe Cys Glu Pro
Gly Asn Val Glu 245 250 255 Asn Asn Gly Val Leu Ser Phe Ile Lys His
Val Leu Phe Pro Leu Lys 260 265 270 Ser Glu Phe Val Ile Leu Arg Asp
Glu Lys Trp Gly Gly Asn Lys Thr 275 280 285 Tyr Thr Ala Tyr Val Asp
Leu Glu Lys Asp Phe Ala Ala Glu Val Val 290 295 300 His Pro Gly Asp
Leu Lys Asn Ser Val Glu Val Ala Leu Asn Lys Leu305 310 315 320 Leu
Asp Pro Ile Arg Glu Lys Phe Asn Thr Pro Ala Leu Lys Lys Leu 325 330
335 Ala Ser Ala Ala Tyr Pro Asp Pro Ser Lys Gln Lys Pro Met Ala Lys
340 345 350 Gly Pro Ala Lys Asn Ser Glu Pro Glu Glu Val Ile Pro Ser
Arg Leu 355 360 365 Asp Ile Arg Val Gly Lys Ile Ile Thr Val Glu Lys
His Pro Asp Ala 370 375 380 Asp Ser Leu Tyr Val Glu Lys Ile Asp Val
Gly Glu Ala Glu Pro Arg385 390 395 400 Thr Val Val Ser Gly Leu Val
Gln Phe Val Pro Lys Glu Glu Leu Gln 405 410 415 Asp Arg Leu Val Val
Val Leu Cys Asn Leu Lys Pro Gln Lys Met Arg 420 425 430 Gly Val Glu
Ser Gln Gly Met Leu Leu Cys Ala Ser Ile Glu Gly Ile 435 440 445 Asn
Arg Gln Val Glu Pro Leu Asp Pro Pro Ala Gly Ser Ala Pro Gly 450 455
460 Glu His Val Phe Val Lys Gly Tyr Glu Lys Gly Gln Pro Asp Glu
Glu465 470 475 480 Leu Lys Pro Lys Lys Lys Val Phe Glu Lys Leu Gln
Ala Asp Phe Lys 485 490 495 Ile Ser Glu Glu Cys Ile Ala Gln Trp Lys
Gln Thr Asn Phe Met Thr 500 505 510 Lys Leu Gly Ser Ile Ser Cys Lys
Ser Leu Lys Gly Gly Asn Ile Ser 515 520 525 21683DNAHomo sapiens
2atgggggacg ctcccagccc tgaagagaaa ctgcacctta tcacccggaa cctgcaggag
60gttctggggg aagagaagct gaaggagata ctgaaggagc gggaacttaa aatttactgg
120ggaacggcaa ccacgggcaa accacatgtg gcttactttg tgcccatgtc
aaagattgca 180gacttcttaa aggcagggtg tgaggtaaca attctgtttg
cggacctcca cgcatacctg 240gataacatga aagccccatg ggaacttcta
gaactccgag tcagttacta tgagaatgtg 300atcaaagcaa tgctggagag
cattggtgtg cccttggaga agctcaagtt catcaaaggc 360actgattacc
agctcagcaa agagtacaca ctagatgtgt acagactctc ctccgtggtc
420acacagcacg attccaagaa ggctggagct gaggtggtaa agcaggtgga
gcaccctttg 480ctgagtggcc tcttataccc cggactgcag gctttggatg
aagagtattt aaaagtagat 540gcccaatttg gaggcattga tcagagaaag
attttcacct ttgcagagaa gtacctccct 600gcacttggct attcaaaacg
ggtccatctg atgaatccta tggttccagg attaacaggc 660agcaaaatga
gctcttcaga agaggagtcc aagattgatc tccttgatcg gaaggaggat
720gtgaagaaaa aactgaagaa ggccttctgt gagccaggaa atgtggagaa
caatggggtt 780ctgtccttca tcaagcatgt cctttttccc cttaagtccg
agtttgtgat cctacgagat 840gagaaatggg gtggaaacaa aacctacaca
gcttacgtgg acctggaaaa ggactttgct 900gctgaggttg tacatcctgg
agacctgaag aattctgttg aagtcgcact gaacaagttg 960ctggatccaa
tccgggaaaa gtttaatacc cctgccctga aaaaactggc cagcgctgcc
1020tacccagatc cctcaaagca gaagccaatg gccaaaggcc ctgccaagaa
ttcagaacca 1080gaggaggtca tcccatcccg gctggatatc cgtgtgggga
aaatcatcac tgtggagaag 1140cacccagatg cagacagcct gtatgtagag
aagattgacg tgggggaagc tgaaccacgg 1200actgtggtga gcggcctggt
acagttcgtg cccaaggagg aactgcagga caggctggta 1260gtggtgctgt
gcaacctgaa accccagaag atgagaggag tcgagtccca aggcatgctt
1320ctgtgtgctt ctatagaagg gataaaccgc caggttgaac ctctggaccc
tccggcaggc 1380tctgctcctg gtgagcacgt gtttgtgaag ggctatgaaa
agggccaacc agatgaggag 1440ctcaagccca agaagaaagt cttcgagaag
ttgcaggctg acttcaaaat ttctgaggag 1500tgcatcgcac agtggaagca
aaccaacttc atgaccaagc tgggctccat ttcctgtaaa 1560tcgctgaaag
gggggaacat tagctagcca gcccagcatc ttcccccctt cttccaccac
1620tgagtcatct gctgtctctt cagtctgctc catccatcac ccatttaccc
atctctcagg 1680aca 16833364PRTHomo sapiens 3Met Gly Asp Ala Pro Ser
Pro Glu Glu Lys Leu His Leu Ile Thr Arg1 5 10 15 Asn Leu Gln Glu
Val Leu Gly Glu Glu Lys Leu Lys Glu Ile Leu Lys 20 25 30 Glu Arg
Glu Leu Lys Ile Tyr Trp Gly Thr Ala Thr Thr Gly Lys Pro 35 40 45
His Val Ala Tyr Phe Val Pro Met Ser Lys Ile Ala Asp Phe Leu Lys 50
55 60 Ala Gly Cys Glu Val Thr Ile Leu Phe Ala Asp Leu His Ala Tyr
Leu65 70 75 80 Asp Asn Met Lys Ala Pro Trp Glu Leu Leu Glu Leu Arg
Val Ser Tyr 85 90 95 Tyr Glu Asn Val Ile Lys Ala Met Leu Glu Ser
Ile Gly Val Pro Leu 100 105 110 Glu Lys Leu Lys Phe Ile Lys Gly Thr
Asp Tyr Gln Leu Ser Lys Glu 115 120 125 Tyr Thr Leu Asp Val Tyr Arg
Leu Ser Ser Val Val Thr Gln His Asp 130 135 140 Ser Lys Lys Ala Gly
Ala Glu Val Val Lys Gln Val Glu His Pro Leu145 150 155 160 Leu Ser
Gly Leu Leu Tyr Pro Gly Leu Gln Ala Leu Asp Glu Glu Tyr 165 170 175
Leu Lys Val Asp Ala Gln Phe Gly Gly Ile Asp Gln Arg Lys Ile Phe 180
185 190 Thr Phe Ala Glu Lys Tyr Leu Pro Ala Leu Gly Tyr Ser Lys Arg
Val 195 200 205 His Leu Met Asn Pro Met Val Pro Gly Leu Thr Gly Ser
Lys Met Ser 210 215 220 Ser Ser Glu Glu Glu Ser Lys Ile Asp Leu Leu
Asp Arg Lys Glu Asp225 230 235 240 Val Lys Lys Lys Leu Lys Lys Ala
Phe Cys Glu Pro Gly Asn Val Glu 245 250 255 Asn Asn Gly Val Leu Ser
Phe Ile Lys His Val Leu Phe Pro Leu Lys 260 265 270 Ser Glu Phe Val
Ile Leu Arg Asp Glu Lys Trp Gly Gly Asn Lys Thr 275 280 285 Tyr Thr
Ala Tyr Val Asp Leu Glu Lys Asp Phe Ala Ala Glu Val Val 290 295 300
His Pro Gly Asp Leu Lys Asn Ser Val Glu Val Ala Leu Asn Lys Leu305
310 315 320 Leu Asp Pro Ile Arg Glu Lys Phe Asn Thr Pro Ala Leu Lys
Lys Leu 325 330 335 Ala Ser Ala Ala Tyr Pro Asp Pro Ser Lys Gln Lys
Pro Met Ala Lys 340 345 350 Gly Pro Ala Lys Asn Ser Glu Pro Glu Glu
Val Ile 355 360 4361PRTArtificial SequenceVariant of mini-YRS
(human tyrosyle tRNA synthatase) 4Met Gly Asp Ala Pro Ser Pro Glu
Glu Lys Leu His Leu Ile Thr Arg1 5 10 15 Asn Leu Gln Glu Val Leu
Gly Glu Glu Lys Leu Lys Glu Ile Leu Lys 20 25 30 Glu Arg Glu Leu
Lys Ile Tyr Trp Gly Thr Ala Thr Thr Gly Lys Pro 35 40 45 His Val
Ala Tyr Phe Val Pro Met Ser Lys Ile Ala Asp Phe Leu Lys 50 55 60
Ala Gly Cys Glu Val Thr Ile Leu Phe Ala Asp Leu His Ala Tyr Leu65
70 75 80 Asp Asn Met Lys Ala Pro Trp Glu Leu Leu Glu Leu Arg Val
Ser Tyr 85 90 95 Tyr Glu Asn Val Ile Lys Ala Met Leu Glu Ser Ile
Gly Val Pro Leu 100 105 110 Glu Lys Leu Lys Phe Ile Lys Gly Thr Asp
Tyr Gln Leu Ser Lys Glu 115 120 125 Tyr Thr Leu Asp Val Tyr Arg Leu
Ser Ser Val Val Thr Gln His Asp 130 135 140 Ser Lys Lys Ala Gly Ala
Glu Val Val Lys Gln Val Glu His Ser Gly 145 150 155 160 Leu Leu Tyr
Pro Gly Leu Gln Ala Leu Asp Glu Glu Tyr Leu Lys Val 165 170 175 Asp
Ala Gln Phe Gly Gly Ile Asp Gln Arg Lys Ile Phe Thr Phe Ala 180 185
190 Glu Lys Tyr Leu Pro Ala Leu Gly Tyr Ser Lys Arg Val His Leu Met
195 200 205 Asn Pro Met Val Pro Gly Leu Thr Gly Ser Lys Met Ser Ser
Ser Glu 210 215 220 Glu Glu Ser Lys Ile Asp Leu Leu Asp Arg Lys Glu
Asp Val Lys Lys225 230 235 240 Lys Leu Lys Lys Ala Phe Cys Glu Pro
Gly Asn Val Glu Asn Asn Gly 245 250 255 Val Leu Ser Phe Ile Lys His
Val Leu Phe Pro Leu Lys Ser Glu Phe 260 265 270 Val Ile Leu Arg Asp
Glu Lys Trp Gly Gly Asn Lys Thr Tyr Thr Ala 275 280 285 Tyr Val Asp
Leu Glu Lys Asp Phe Ala Ala Glu Val Val His Pro Gly 290 295 300 Asp
Leu Lys Asn Ser Val Glu Val Ala Leu Asn Lys Leu Leu Asp Pro305 310
315 320 Ile Arg Glu Lys Phe Asn Thr Pro Ala Leu Lys Lys Leu Ala Ser
Ala 325 330 335 Ala Tyr Pro Asp Pro Ser Lys Gln Lys Pro Met Ala Lys
Gly Pro Ala 340 345 350 Lys Asn Ser Glu Pro Glu Glu Val Ile 355 360
5471PRTHomo sapiens 5Met Pro Asn Ser Glu Pro Ala Ser Leu Leu Glu
Leu Phe Asn Ser Ile1 5 10 15 Ala Thr Gln Gly Glu Leu Val Arg Ser
Leu Lys Ala Gly Asn Ala Ser 20 25 30 Lys Asp Glu Ile Asp Ser Ala
Val Lys Met Leu Val Ser Leu Lys Met 35 40 45 Ser Tyr Lys Ala Ala
Ala Gly Glu Asp Tyr Lys Ala Asp Cys Pro Pro 50 55 60 Gly Asn Pro
Ala Pro Thr Ser Asn His Gly Pro Asp Ala Thr Glu Ala65 70 75 80 Glu
Glu Asp Phe Val Asp Pro Trp Thr Val Gln Thr Ser Ser Ala Lys 85 90
95 Gly Ile Asp Tyr Asp Lys Leu Ile Val Arg Phe Gly Ser Ser Lys Ile
100 105 110 Asp Lys Glu Leu Ile Asn Arg Ile Glu Arg Ala Thr Gly Gln
Arg Pro 115 120 125 His His Phe Leu Arg Arg Gly Ile Phe Phe Ser His
Arg Asp Met Asn 130 135 140 Gln Val Leu Asp Ala Tyr Glu Asn Lys Lys
Pro Phe Tyr Leu Tyr Thr145 150 155 160 Gly Arg Gly Pro Ser Ser Glu
Ala Met His Val Gly His Leu Ile Pro 165 170 175 Phe Ile Phe Thr Lys
Trp Leu Gln Asp Val Phe Asn Val Pro Leu Val 180 185 190 Ile Gln Met
Thr Asp Asp Glu Lys Tyr Leu Trp Lys Asp Leu Thr Leu 195 200 205 Asp
Gln Ala Tyr Ser Tyr Ala Val Glu Asn Ala Lys Asp Ile Ile Ala 210 215
220 Cys Gly Phe Asp Ile Asn Lys Thr Phe Ile Phe Ser Asp Leu Asp
Tyr225 230 235 240 Met Gly Met Ser Ser Gly Phe Tyr Lys Asn Val Val
Lys Ile Gln Lys 245 250 255 His Val Thr Phe Asn Gln Val Lys Gly Ile
Phe Gly Phe Thr Asp Ser 260 265 270 Asp Cys Ile Gly Lys Ile Ser Phe
Pro Ala Ile Gln Ala Ala Pro Ser 275 280 285 Phe Ser Asn Ser Phe Pro
Gln Ile Phe Arg Asp Arg Thr Asp Ile Gln 290 295 300 Cys Leu Ile Pro
Cys Ala Ile Asp Gln Asp Pro Tyr Phe Arg Met Thr305 310 315 320 Arg
Asp Val Ala Pro Arg Ile Gly Tyr Pro Lys Pro Ala Leu Leu His 325 330
335 Ser Thr Phe Phe Pro Ala Leu Gln Gly Ala Gln Thr Lys Met Ser Ala
340 345 350 Ser Asp Pro Asn Ser Ser Ile Phe Leu Thr Asp Thr Ala Lys
Gln Ile 355 360 365 Lys Thr Lys Val Asn Lys His Ala Phe Ser Gly Gly
Arg Asp Thr Ile 370 375 380 Glu Glu His Arg Gln Phe Gly Gly Asn Cys
Asp Val Asp Val Ser Phe385 390 395 400 Met Tyr Leu Thr Phe Phe Leu
Glu Asp Asp Asp Lys Leu Glu Gln Ile 405 410 415 Arg Lys Asp Tyr Thr
Ser Gly Ala Met Leu Thr Gly Glu Leu Lys Lys 420 425 430 Ala Leu Ile
Glu Val Leu Gln Pro Leu Ile Ala Glu His Gln Ala Arg 435 440 445 Arg
Lys Glu Val Thr Asp Glu Ile Val Lys Glu Phe Met Thr Pro Arg 450 455
460 Lys Leu Ser Phe Asp Phe Gln465 470 61959DNAHomo sapiens
6cgaaaaaaga ggggaagagt attaaagacc atttctggct gggcagggca ctctcagcag
60ctcaactgcc cagcgtgacc agtggccacc tctgcagtgt cttccacaac ctggtcttga
120ctcgtctgct gaacaaatcc tctgacctca ggccggctgt gaacgtagtt
cctgagagat 180agcaaacatg cccaacagtg agcccgcatc tctgctggag
ctgttcaaca gcatcgccac 240acaaggggag ctcgtaaggt ccctcaaagc
gggaaatgcg tcaaaggatg aaattgattc 300tgcagtaaag atgttggtgt
cattaaaaat gagctacaaa gctgccgcgg gggaggatta 360caaggctgac
tgtcctccag ggaacccagc acctaccagt aatcatggcc cagatgccac
420agaagctgaa gaggattttg tggacccatg gacagtacag acaagcagtg
caaaaggcat 480agactacgat aagctcattg ttcggtttgg aagtagtaaa
attgacaaag agctaataaa 540ccgaatagag agagccaccg gccaaagacc
acaccacttc ctgcgcagag gcatcttctt 600ctcacacaga gatatgaatc
aggttcttga tgcctatgaa aataagaagc cattttatct 660gtacacgggc
cggggcccct cttctgaagc aatgcatgta ggtcacctca ttccatttat
720tttcacaaag tggctccagg atgtatttaa cgtgcccttg gtcatccaga
tgacggatga 780cgagaagtat ctgtggaagg acctgaccct ggaccaggcc
tatggcgatg ctgttgagaa 840tgccaaggac atcatcgcct gtggctttga
catcaacaag actttcatat tctctgacct 900ggactacatg gggatgagct
caggtttcta caaaaatgtg gtgaagattc aaaagcatgt 960taccttcaac
caagtgaaag gcattttcgg cttcactgac agcgactgca ttgggaagat
1020cagttttcct gccatccagg ctgctccctc cttcagcaac tcattcccac
agatcttccg 1080agacaggacg gatatccagt gccttatccc atgtgccatt
gaccaggatc cttactttag 1140aatgacaagg gacgtcgccc ccaggatcgg
ctatcctaaa ccagccctgt tgcactccac 1200cttcttccca gccctgcagg
gcgcccagac caaaatgagt gccagcgacc caaactcctc 1260catcttcctc
accgacacgg ccaagcagat caaaaccaag gtcaataagc atgcgttttc
1320tggagggaga gacaccatcg aggagcacag gcagtttggg ggcaactgtg
atgtggacgt 1380gtctttcatg tacctgacct tcttcctcga ggacgacgac
aagctcgagc agatcaggaa 1440ggattacacc agcggagcca tgctcaccgg
tgagctcaag aaggcactca tagaggttct 1500gcagcccttg atcgcagagc
accaggcccg gcgcaaggag gtcacggatg agatagtgaa 1560agagttcatg
actccccgga agctgtcctt cgactttcag tagcactcgt tttacatatg
1620cttataaaag aagtgatgta tcagtaatgt atcaataatc ccagcccagt
caaagcaccg 1680ccacctgtag gcttctgtct catggtaatt actgggcctg
gcctctgtaa gcctgtgtat 1740gttatcaata ctgtttcttc ctgtgagttc
cattatttct atctcttatg ggcaaagcat 1800tgtgggtaat tggtgctggc
taacattgca tggtcggata gagaagtcca gctgtgagtc 1860tctccccaaa
gcagccccac agtggagcct tcggctggaa gtccatgggc caccctgttc
1920ttgtccatgg aggacttccg agggttccaa gtatactct
19597381PRTHomo sapiens 7Gln Thr Ser Ser Ala Lys Gly Ile Asp Tyr
Asp Lys Leu Ile Val Arg1 5 10 15 Phe Gly Ser Ser Lys Ile Asp Lys
Glu Leu Ile Asn Arg Ile Glu Arg 20 25 30 Ala Thr Gly Gln Arg Pro
His His Phe Leu Arg Arg Gly Ile Phe Phe 35 40 45 Ser His Arg Asp
Met Asn Gln Val Leu Asp Ala Tyr Glu Asn Lys Lys 50 55 60 Pro Phe
Tyr Leu Tyr Thr Gly Arg Gly Pro Ser Ser Glu Ala Met His65 70 75 80
Val Gly His Leu Ile Pro Phe Ile Phe Thr Lys Trp Leu Gln Asp Val 85
90 95 Phe Asn Val Pro Leu Val Ile Gln Met Thr Asp Asp Glu Lys Tyr
Leu 100 105 110 Trp Lys Asp Leu Thr Leu Asp Gln Ala Tyr Ser Tyr Ala
Val Glu Asn 115 120 125 Ala Lys Asp Ile Ile Ala Cys Gly Phe Asp Ile
Asn Lys Thr Phe Ile 130 135 140 Phe Ser Asp Leu Asp Tyr Met Gly Met
Ser Ser Gly Phe Tyr Lys Asn145 150 155 160 Val Val Lys Ile Gln Lys
His Val Thr Phe Asn Gln Val Lys Gly Ile 165 170 175 Phe Gly Phe Thr
Asp Ser Asp Cys Ile Gly Lys Ile Ser Phe Pro Ala 180 185 190 Ile Gln
Ala Ala Pro Ser Phe Ser Asn Ser Phe Pro Gln Ile Phe Arg 195 200 205
Asp Arg Thr Asp Ile Gln Cys Leu Ile Pro Cys Ala Ile Asp Gln Asp 210
215 220 Pro Tyr Phe Arg Met Thr Arg Asp Val Ala Pro Arg Ile Gly Tyr
Pro225 230 235 240 Lys Pro Ala Leu Leu His Ser Thr Phe Phe Pro Ala
Leu Gln Gly Ala 245 250 255 Gln Thr Lys Met Ser Ala Ser Asp Pro Asn
Ser Ser Ile Phe Leu Thr 260 265 270 Asp Thr Ala Lys Gln Ile Lys Thr
Lys Val Asn Lys His Ala Phe Ser 275 280 285 Gly Gly Arg Asp Thr Ile
Glu Glu His Arg Gln Phe Gly Gly Asn Cys 290 295 300 Asp Val Asp Val
Ser Phe Met Tyr Leu Thr Phe Phe Leu Glu Asp Asp305 310 315 320 Asp
Lys Leu Glu Gln Ile Arg Lys Asp Tyr Thr Ser Gly Ala Met Leu 325 330
335 Thr Gly Glu Leu Lys Lys Ala Leu Ile Glu Val Leu Gln Pro Leu Ile
340 345 350 Ala Glu His Gln Ala Arg Arg Lys Glu Val Thr Asp Glu Ile
Val Lys 355 360 365 Glu Phe Met Thr Pro Arg Lys Leu Ser Phe Asp Phe
Gln 370 375 380 8378PRTArtificial SequenceModified T2-WRS (human
tryptophanyl tRNA synthatase) 8Ser Ala Lys Gly Ile Asp Tyr Asp Lys
Leu Ile Val Arg Phe Gly Ser1 5 10 15 Ser Lys Ile Asp Lys Glu Leu
Ile Asn Arg Ile Glu Arg Ala Thr Gly 20 25 30 Gln Arg Pro His His
Phe Leu Arg Arg Gly Ile Phe Phe Ser His Arg 35 40 45 Asp Met Asn
Gln Val Leu Asp Ala Tyr Glu Asn Lys Lys Pro Phe Tyr 50 55 60 Leu
Tyr Thr Gly Arg Gly Pro Ser Ser Glu Ala Met His Val Gly His65 70 75
80 Leu Ile Pro Phe Ile Phe Thr Lys Trp Leu Gln Asp Val Phe Asn Val
85 90 95 Pro Leu Val Ile Gln Met Thr Asp Asp Glu Lys Glu Leu Trp
Lys Asp 100 105 110 Leu Thr Leu Asp Gln Ala Tyr Ser Tyr Ala Val Glu
Asn Ala Lys Asp 115 120 125 Ile Ile Ala Cys Gly Phe Asp Ile Asn Lys
Thr Phe Ile Phe Ser Asp 130 135 140 Leu Asp Tyr Met Gly Met Ser Ser
Gly Phe Tyr Lys Asn Val Val Lys145 150 155 160 Ile Gln Lys His Val
Thr Glu Asn Gln Val Lys Gly Ile Phe Gly Phe 165 170 175 Thr Asp Ser
Asp Cys Ile Gly Lys Glu Ser Phe Pro Ala Ile Gln Ala 180 185 190 Ala
Pro Ser Phe Ser Asn Ser Phe Pro Gln Ile Phe Arg Asp Arg Thr 195 200
205 Asp Ile Gln Cys Leu Ile Pro Cys Ala Ile Asp Gln Asp Pro Tyr Phe
210 215 220 Arg Met Thr Arg Asp Val Ala Pro Arg Ile Gly Tyr Pro Lys
Pro Ala225 230 235 240 Leu Leu His Ser Thr Phe Phe Pro Ala Leu Gln
Gly Ala Gln Thr Lys 245 250 255 Met Ser Ala Ser Asp Pro Asn Ser Ser
Ile Phe Leu Thr Asp Thr Ala 260 265 270 Lys Gln Ile Lys Thr Lys Val
Asn Lys His Ala Phe Ser Gly Gly Arg 275 280 285 Asp Thr Ile Glu Glu
His Arg Gln Phe Gly Gly Asn Cys Asp Val Asp 290 295 300 Val Ser Phe
Met Tyr Leu Thr Phe Phe Leu Glu Asp Asp Asp Lys Leu305 310 315 320
Glu Gln Ile Arg Lys Asp Tyr Thr Ser Gly Ala Met Leu Thr Gly Glu 325
330 335 Leu Lys Lys Ala Leu Ile Glu Val Leu Gln Pro Leu Ile Ala Glu
His 340 345 350 Gln Ala Arg Arg Lys Glu Val Thr Asp Glu Ile Val Lys
Glu Phe Met 355 360 365 Thr Pro Arg Lys Leu Ser Phe Asp Phe Gln 370
375 9378PRTArtificial SequenceModified T2-WRS (human tryptophanyl
tRNA synthatase) 9Ser Ala Lys Gly Ile Asp Tyr Asp Lys Leu Ile Val
Arg Phe Gly Ser1 5 10 15 Ser Lys Ile Asp Lys Glu Leu Ile Asn Arg
Ile Glu Arg Ala Thr Gly 20 25 30 Gln Arg Pro His His Phe Leu Arg
Arg Gly Ile Phe Phe Ser His Arg 35 40 45 Asp Met Asn Gln Val Leu
Asp Ala Tyr Glu Asn Lys Lys Pro Phe Tyr 50 55 60 Leu Tyr Thr Gly
Arg Gly Pro Ser Ser Glu Ala Met His Val Gly His65 70 75 80 Leu Ile
Pro Phe Ile Phe Thr Lys Trp Leu Gln Asp Val Phe Asn Val 85 90 95
Pro Leu Val Ile Gln Met Thr Asp Asp Glu Lys Glu Leu Trp Lys Asp 100
105 110 Leu Thr Leu Asp Gln Ala Tyr Ser Tyr Ala Val Glu Asn Ala Lys
Asp 115 120 125 Ile Ile Ala Cys Gly Phe Asp Ile Asn Lys Thr Phe Ile
Phe Ser Asp 130 135 140 Leu Asp Tyr Met Gly Met Ser Ser Gly Phe Tyr
Lys Asn Val Val Lys145 150 155 160 Ile Gln Lys His Val Thr Glu Asn
Gln Val Lys Gly Ile Phe Gly Phe 165 170 175 Thr Asp Ser Asp Cys Ile
Gly Lys Ile Ser Phe Pro Ala Ile Gln Ala 180 185 190 Ala Pro Ser Phe
Ser Asn Ser Phe Pro Gln Ile Phe Arg Asp Arg Thr 195 200 205 Asp Ile
Gln Cys Leu Ile Pro Cys Ala Ile Asp Gln Asp Pro Tyr Phe 210 215 220
Arg Met Thr Arg Asp Val Ala Pro Arg Ile Gly Tyr Pro Lys Pro Ala225
230 235 240 Leu Leu His Ser Thr Phe Phe Pro Ala Leu Gln Gly Ala Gln
Thr Lys 245 250 255 Met Ser Ala Ser Asp Pro Asn Ser Ser Ile Phe Leu
Thr Asp Thr Ala 260 265 270 Lys Gln Ile Lys Thr Lys Val Asn Lys His
Ala Phe Ser Gly Gly Arg 275 280 285 Asp Thr Ile Glu Glu His Arg Gln
Phe Gly Gly Asn Cys Asp Val Asp 290 295 300 Val Ser Phe Met Tyr Leu
Thr Phe Phe Leu Glu Asp Asp Asp Lys Leu305 310 315 320 Glu Gln Ile
Arg Lys Asp Tyr Thr Ser Gly Ala Met Leu Thr Gly Glu 325 330 335 Leu
Lys Lys Ala Leu Ile Glu Val Leu Gln Pro Leu Ile Ala Glu His 340 345
350 Gln Ala Arg Arg Lys Glu Val Thr Asp Glu Ile Val Lys Glu Phe Met
355 360 365 Thr Pro Arg Lys Leu Ser Phe Asp Phe Gln 370 375
10108PRTHomo sapiens 10Asp Trp Ile Trp Asn Gln Met His Ile Asp Glu
Glu Lys Asn Thr Ser1 5 10 15 Leu Pro His His Val Gly Lys Ile Lys
Ser Ser Val Ser Arg Lys Asn 20 25 30 Ala Lys Tyr Leu Leu Lys Gly
Glu Tyr Val Gly Lys Val Phe Arg Val 35 40 45 Asp Ala Glu Thr Gly
Asp Val Phe Ala Ile Glu Arg Leu Asp Arg Glu 50 55 60 Asn Ile Ser
Glu Tyr His Leu Thr Ala Val Ile Val Asp Lys Asp Thr65 70 75 80 Gly
Glu Asn Leu Glu Thr Pro Ser Ser Phe Thr Ile Lys Val His Asp 85 90
95 Val Asn Asp Asn Trp Pro Val Phe Thr His Arg Leu 100 105
11597PRTHomo sapiens 11Met Ala Ala Val Gln Ala Ala Glu Val Lys Val
Asp Gly Ser Glu Pro1 5 10 15 Lys Leu Ser Lys Asn Glu Leu Lys Arg
Arg Leu Lys Ala Glu Lys Lys 20 25 30 Val Ala Glu Lys Glu Ala Lys
Gln Lys Glu Leu Ser Glu Lys Gln Leu 35 40 45 Ser Gln Ala Thr Ala
Ala Ala Thr Asn His Thr Thr Asp Asn Gly Val 50 55 60 Gly Pro Glu
Glu Glu Ser Val Asp Pro Asn Gln Tyr Tyr Lys Ile Arg65 70 75 80 Ser
Gln Ala Ile His Gln Leu Lys Val Asn Gly Glu Asp Pro Tyr Pro 85 90
95 His Lys Phe His Val Asp Ile Ser Leu Thr Asp Phe Ile Gln Lys Tyr
100 105 110 Ser His Leu Gln Pro Gly Asp His Leu Thr Asp Ile Thr Leu
Lys Val 115 120 125 Ala Gly Arg Ile His Ala Lys Arg Ala Ser Gly Gly
Lys Leu Ile Phe 130 135 140 Tyr Asp Leu Arg Gly Glu Gly Val Lys Leu
Gln Val Met Ala Asn Ser145 150 155 160 Arg Asn Tyr Lys Ser Glu Glu
Glu Phe Ile His Ile Asn Asn Lys Leu 165 170 175 Arg Arg Gly Asp Ile
Ile Gly Val Gln Gly Asn Pro Gly Lys Thr Lys 180 185 190 Lys Gly Glu
Leu Ser Ile Ile Pro Tyr Glu Ile Thr Leu Leu Ser Pro 195 200 205 Cys
Leu His Met Leu Pro His Leu His Phe Gly Leu Lys Asp Lys Glu 210 215
220 Thr Arg Tyr Arg Gln Arg Tyr Leu Asp Leu Ile Leu Asn Asp Phe
Val225 230 235 240 Arg Gln Lys Phe Ile Ile Arg Ser Lys Ile Ile Thr
Tyr Ile Arg Ser 245 250 255 Phe Leu Asp Glu Leu Gly Phe Leu Glu Ile
Glu Thr Pro Met Met Asn 260 265 270 Ile Ile Pro Gly Gly Ala Val Ala
Lys Pro Phe Ile Thr Tyr His Asn 275 280 285 Glu Leu Asp Met Asn Leu
Tyr Met Arg Ile Ala Pro Glu Leu Tyr His 290 295 300 Lys Met Leu Val
Val Gly Gly Ile Asp Arg Val Tyr Glu Ile Gly Arg305 310 315 320 Gln
Phe Arg Asn Glu Gly Ile Asp Leu Thr His Asn Pro Glu Phe Thr 325 330
335 Thr Cys Glu Phe Tyr Met Ala Tyr Ala Asp Tyr His Asp Leu Met Glu
340 345 350 Ile Thr Glu Lys Met Val Ser Gly Met Val Lys His Ile Thr
Gly Ser 355 360 365 Tyr Lys Val Thr Tyr His Pro Asp Gly Pro Glu Gly
Gln Ala Tyr Asp 370 375 380 Val Asp Phe Thr Pro Pro Phe Arg Arg Ile
Asn Met Val Glu Glu Leu385 390 395 400 Glu Lys Ala Leu Gly Met Lys
Leu Pro Glu Thr Asn Leu Phe Glu Thr 405 410 415 Glu Glu Thr Arg Lys
Ile Leu Asp Asp Ile Cys Val Ala Lys Ala Val 420 425 430 Glu Cys Pro
Pro Pro Arg Thr Thr Ala Arg Leu Leu Asp Lys Leu Val 435 440 445 Gly
Glu Phe Leu Glu Val Thr Cys Ile Asn Pro Thr Phe Ile Cys Asp 450 455
460 His Pro Gln Ile Met Ser Pro Leu Ala Lys Trp His Arg Ser Lys
Glu465 470 475 480 Gly Leu Thr Glu Arg Phe Glu Leu Phe Val Met Lys
Lys Glu Ile Cys 485 490 495 Asn Ala Tyr Thr Glu Leu Asn Asp Pro Met
Arg Gln Arg Gln Leu Phe 500 505 510 Glu Glu Gln Ala Lys Ala Lys Ala
Ala Gly Asp Asp Glu Ala Met Phe 515 520 525 Ile Asp Glu Asn Phe Cys
Thr Ala Leu Glu Tyr Gly Leu Pro Pro Thr 530 535 540 Ala Gly Trp Gly
Met Gly Ile Asp Arg Val Ala Met Phe Leu Thr Asp545 550 555 560 Ser
Asn Asn Ile Lys Glu Val Leu Leu Phe Pro Ala Met Lys Pro Glu 565 570
575 Asp Lys Lys Glu Asn Val Ala Thr Thr Asp Thr Leu Glu Ser Thr Thr
580 585 590 Val Gly Thr Ser Val 595 12515PRTHomo sapiens 12Ser Val
Asp Pro Asn Gln Tyr Tyr Lys Ile Arg Ser Gln Ala Ile His1 5 10 15
Gln Leu Lys Val Asn Gly Glu Asp Pro Tyr Pro His Lys Phe His Val 20
25 30 Asp Ile Ser Leu Thr Asp Phe Ile Gln Lys Tyr Ser His Leu Gln
Pro 35 40 45 Gly Asp His Leu Thr Asp Ile Thr Leu Lys Val Ala Gly
Arg Ile His 50 55 60 Ala Lys Arg Ala Ser Gly Gly Lys Leu Ile Phe
Tyr Asp Leu Arg Gly65 70 75 80 Glu Gly Val Lys Leu Gln Val Met Ala
Asn Ser Arg Asn Tyr Lys Ser 85 90 95 Glu Glu Glu Phe Ile His Ile
Asn Asn Lys Leu Arg Arg Gly Asp Ile 100 105 110 Ile Gly Val Gln Gly
Asn Pro Gly Lys Thr Lys Lys Gly Glu Leu Ser 115 120 125 Ile Ile Pro
Tyr Glu Ile Thr Leu Leu Ser Pro Cys Leu His Met Leu 130 135 140 Pro
His Leu His Phe Gly Leu Lys Asp Lys Glu Thr Arg Tyr Arg Gln145 150
155 160 Arg Tyr Leu Asp Leu Ile Leu Asn Asp Phe Val Arg Gln Lys Phe
Ile 165 170 175 Ile Arg Ser Lys Ile Ile Thr Tyr Ile Arg Ser Phe Leu
Asp Glu Leu 180 185 190 Gly Phe Leu Glu Ile Glu Thr Pro Met Met Asn
Ile Ile Pro Gly Gly 195 200 205 Ala Val Ala Lys Pro Phe Ile Thr Tyr
His Asn Glu Leu Asp Met Asn 210 215 220 Leu Tyr Met Arg Ile Ala Pro
Glu Leu Tyr His Lys Met Leu Val Val225 230 235 240 Gly Gly Ile Asp
Arg Val Tyr Glu Ile Gly Arg Gln Phe Arg Asn Glu 245 250 255 Gly Ile
Asp Leu Thr His Asn Pro Glu Phe Thr Thr Cys Glu Phe Tyr 260 265 270
Met Ala Tyr Ala Asp Tyr His Asp Leu Met Glu Ile Thr Glu Lys Met 275
280 285 Val Ser Gly Met Val Lys His Ile Thr Gly Ser Tyr Lys Val Thr
Tyr 290 295 300 His Pro Asp Gly Pro Glu Gly Gln Ala Tyr Asp Val Asp
Phe Thr Pro305 310 315 320 Pro Phe Arg Arg Ile Asn Met Val Glu Glu
Leu Glu Lys Ala Leu Gly 325 330 335 Met Lys Leu Pro Glu Thr Asn Leu
Phe Glu Thr Glu Glu Thr Arg Lys 340 345 350 Ile Leu Asp Asp Ile Cys
Val Ala Lys Ala Val Glu Cys Pro Pro Pro 355 360 365 Arg Thr Thr Ala
Arg Leu Leu Asp Lys Leu Val Gly Glu Phe Leu Glu 370 375 380 Val Thr
Cys Ile Asn Pro Thr Phe Ile Cys Asp His Pro Gln Ile Met385 390 395
400 Ser Pro Leu Ala Lys Trp His Arg Ser Lys Glu Gly Leu Thr Glu Arg
405 410 415 Phe Glu Leu Phe Val Met Lys Lys Glu Ile Cys Asn Ala Tyr
Thr Glu 420 425 430 Leu Asn Asp
Pro Met Arg Gln Arg Gln Leu Phe Glu Glu Gln Ala Lys 435 440 445 Ala
Lys Ala Ala Gly Asp Asp Glu Ala Met Phe Ile Asp Glu Asn Phe 450 455
460 Cys Thr Ala Leu Glu Tyr Gly Leu Pro Pro Thr Ala Gly Trp Gly
Met465 470 475 480 Gly Ile Asp Arg Val Ala Met Phe Leu Thr Asp Ser
Asn Asn Ile Lys 485 490 495 Glu Val Leu Leu Phe Pro Ala Met Lys Pro
Glu Asp Lys Lys Glu Asn 500 505 510 Val Ala Thr 515
13770PRTArtificial SequenceTruncated human KRS with E. coli
flavodoxin protein insert 13Met Ala Ala Val Gln Ala Ala Glu Val Lys
Val Asp Gly Ser Glu Pro1 5 10 15 Lys Leu Ser Lys Asn Glu Leu Lys
Arg Arg Leu Lys Ala Glu Lys Lys 20 25 30 Val Ala Glu Lys Glu Ala
Lys Gln Lys Glu Leu Ser Glu Lys Gln Leu 35 40 45 Ser Gln Ala Thr
Ala Ala Ala Thr Asn His Thr Thr Asp Asn Gly Val 50 55 60 Gly Pro
Glu Glu Glu Ser Val Asp Pro Asn Gln Tyr Tyr Lys Ile Arg65 70 75 80
Ser Gln Ala Ile His Gln Leu Lys Val Asn Gly Glu Asp Pro Tyr Pro 85
90 95 His Lys Phe His Val Asp Ile Ser Leu Thr Asp Phe Ile Gln Lys
Tyr 100 105 110 Ser His Leu Gln Pro Gly Asp His Leu Thr Asp Ile Thr
Leu Lys Val 115 120 125 Ala Gly Arg Ile His Ala Lys Arg Ala Ser Gly
Gly Lys Leu Ile Phe 130 135 140 Tyr Asp Leu Arg Gly Glu Gly Val Lys
Leu Gln Val Met Ala Asn Ser145 150 155 160 Arg Asn Tyr Lys Ser Glu
Glu Glu Phe Ile His Ile Asn Asn Lys Leu 165 170 175 Arg Arg Gly Asp
Ile Ile Gly Val Gln Gly Asn Pro Gly Lys Thr Lys 180 185 190 Lys Gly
Glu Leu Ser Ile Ile Pro Tyr Glu Ile Thr Leu Leu Ser Pro 195 200 205
Cys Leu His Met Leu Pro His Leu His Phe Gly Leu Lys Asp Lys Glu 210
215 220 Thr Arg Tyr Arg Gln Arg Tyr Leu Asp Leu Ile Leu Asn Asp Phe
Val225 230 235 240 Arg Gln Lys Phe Ile Ile Arg Ser Lys Ile Ile Thr
Tyr Ile Arg Ser 245 250 255 Phe Leu Asp Glu Leu Gly Phe Leu Glu Ile
Glu Thr Pro Met Met Asn 260 265 270 Ile Ile Pro Gly Gly Ala Val Ala
Lys Pro Phe Ile Thr Tyr His Asn 275 280 285 Glu Leu Asp Met Asn Leu
Tyr Met Arg Ile Ala Pro Glu Leu Tyr His 290 295 300 Lys Met Leu Val
Val Gly Asn Met Gly Leu Phe Tyr Gly Ser Ser Thr305 310 315 320 Cys
Tyr Thr Glu Met Ala Ala Glu Lys Ile Arg Asp Ile Ile Gly Pro 325 330
335 Glu Leu Val Thr Leu His Asn Leu Lys Asp Asp Ser Pro Lys Leu Met
340 345 350 Glu Gln Tyr Asp Val Leu Ile Leu Gly Ile Pro Thr Trp Asp
Phe Gly 355 360 365 Glu Ile Gln Glu Asp Trp Glu Ala Val Trp Asp Gln
Leu Asp Asp Leu 370 375 380 Asn Leu Glu Gly Lys Ile Val Ala Leu Tyr
Gly Leu Gly Asp Gln Leu385 390 395 400 Gly Tyr Gly Glu Trp Phe Leu
Asp Ala Leu Gly Met Leu His Asp Lys 405 410 415 Leu Ser Thr Lys Gly
Val Lys Phe Val Gly Tyr Trp Pro Thr Glu Gly 420 425 430 Tyr Glu Phe
Thr Ser Pro Lys Pro Val Ile Ala Asp Gly Gln Leu Phe 435 440 445 Val
Gly Leu Ala Leu Asp Glu Thr Asn Gln Tyr Asp Leu Ser Asp Glu 450 455
460 Arg Ile Gln Ser Trp Cys Glu Gln Ile Leu Asn Glu Met Ala Arg
Val465 470 475 480 Tyr Glu Ile Gly Arg Gln Phe Arg Asn Glu Gly Ile
Asp Leu Thr His 485 490 495 Asn Pro Glu Phe Thr Thr Cys Glu Phe Tyr
Met Ala Tyr Ala Asp Tyr 500 505 510 His Asp Leu Met Glu Ile Thr Glu
Lys Met Val Ser Gly Met Val Lys 515 520 525 His Ile Thr Gly Ser Tyr
Lys Val Thr Tyr His Pro Asp Gly Pro Glu 530 535 540 Gly Gln Ala Tyr
Asp Val Asp Phe Thr Pro Pro Phe Arg Arg Ile Asn545 550 555 560 Met
Val Glu Glu Leu Glu Lys Ala Leu Gly Met Lys Leu Pro Glu Thr 565 570
575 Asn Leu Phe Glu Thr Glu Glu Thr Arg Lys Ile Leu Asp Asp Ile Cys
580 585 590 Val Ala Lys Ala Val Glu Cys Pro Pro Pro Arg Thr Thr Ala
Arg Leu 595 600 605 Leu Asp Lys Leu Val Gly Glu Phe Leu Glu Val Thr
Cys Ile Asn Pro 610 615 620 Thr Phe Ile Cys Asp His Pro Gln Ile Met
Ser Pro Leu Ala Lys Trp625 630 635 640 His Arg Ser Lys Glu Gly Leu
Thr Glu Arg Phe Glu Leu Phe Val Met 645 650 655 Lys Lys Glu Ile Cys
Asn Ala Tyr Thr Glu Leu Asn Asp Pro Met Arg 660 665 670 Gln Arg Gln
Leu Phe Glu Glu Gln Ala Lys Ala Lys Ala Ala Gly Asp 675 680 685 Asp
Glu Ala Met Phe Ile Asp Glu Asn Phe Cys Thr Ala Leu Glu Tyr 690 695
700 Gly Leu Pro Pro Thr Ala Gly Trp Gly Met Gly Ile Asp Arg Val
Ala705 710 715 720 Met Phe Leu Thr Asp Ser Asn Asn Ile Lys Glu Val
Leu Leu Phe Pro 725 730 735 Ala Met Lys Pro Glu Asp Lys Lys Glu Asn
Val Ala Thr Thr Asp Thr 740 745 750 Leu Glu Ser Thr Thr Val Gly Thr
Ser Val Ala Gly His His His His 755 760 765 His His 770
142310DNAArtificial SequenceTruncated human KRS with E. coli
flavodoxin insert 14atggcagctg ttcaagcggc ggaagttaaa gttgacggta
gcgaacctaa actgagcaaa 60aacgaactta aacgtcgtct gaaggcggaa aaaaaagtag
cggaaaagga agctaaacag 120aaagaactga gcgaaaaaca gctgtcccag
gctactgcgg ctgcgactaa ccataccact 180gacaacggtg taggtcctga
agaagaatct gttgacccga accagtacta taaaatccgt 240agccaagcga
tccaccagct taaagttaac ggtgaagacc catacccgca caaattccac
300gttgacatta gcctgacgga cttcatccag aaatactctc atctgcagcc
gggtgatcat 360ctgactgaca tcaccttgaa agtcgcgggt cgtatccatg
ctaaacgtgc tagcggtggt 420aaactgatct tctacgatct gcgtggcgaa
ggtgttaaac tgcaggttat ggcaaactct 480cgtaactaca aatctgaaga
agaattcatc cacattaaca acaaactgcg tcgtggtgac 540atcatcggtg
ttcagggtaa cccgggcaaa actaaaaaag gtgaacttag catcatcccg
600tatgaaatca ccctgttgtc cccgtgcctg cacatgctgc ctcacctgca
cttcggtctt 660aaagataaag aaacccgtta ccgtcagcgt taccttgacc
tgatcctgaa tgacttcgtt 720cgtcagaaat tcatcatccg ttctaaaatc
atcacctata tccgtagctt cctggacgaa 780ctgggtttcc tggagattga
gaccccgatg atgaacatca ttccgggtgg tgcggttgct 840aagccgttca
tcacctacca taacgaactt gacatgaacc tgtacatgcg tatcgctccg
900gaactgtacc acaaaatgct ggttgtaggt aatatgggtc ttttttacgg
ttccagcacc 960tgttacaccg aaatggcggc agaaaaaatc cgcgatatta
tcggcccaga actggtgacc 1020ttacataacc tcaaggacga ctccccgaaa
ttaatggagc agtacgatgt gctcattctg 1080ggtatcccga cctgggattt
tggtgaaatc caggaagact gggaagccgt ctgggatcag 1140ctcgacgacc
tgaaccttga aggtaaaatt gttgcgctgt atgggcttgg cgatcaactg
1200ggatacggcg agtggttcct cgatgcgctc ggtatgctgc atgacaaact
ctcgaccaaa 1260ggcgtgaagt tcgtcggcta ctggccaacg gaaggatatg
aatttaccag cccgaaaccg 1320gtgattgctg acgggcaact gttcgtgggt
ctggcgctgg atgaaactaa ccagtatgac 1380cttagcgacg agcgtattca
gagctggtgc gagcaaatcc tcaacgaaat ggcacgtgtg 1440tatgaaatcg
gtcgtcagtt tcgtaacgag ggtattgacc tgacccataa cccggaattc
1500accacctgcg aattctacat ggcatacgct gattaccacg acctgatgga
aatcactgaa 1560aaaatggtta gcggtatggt taaacacatc accggtagct
ataaagtgac ctaccacccg 1620gacggccctg aaggtcaagc gtatgacgtt
gacttcaccc cgccgtttcg tcgtattaac 1680atggttgaag aacttgaaaa
agctctgggt atgaaactgc ctgaaactaa cctgttcgaa 1740accgaagaaa
cccgtaaaat cctggacgac atctgcgtag ctaaagctgt tgaatgccct
1800ccgccgcgta ccaccgctcg tctgcttgac aaactggttg gtgaattcct
tgaagtaacc 1860tgcattaacc cgaccttcat ttgcgaccac ccacagatca
tgtctccgct ggctaaatgg 1920caccgttcta aagaaggtct gaccgaacgt
tttgaactgt tcgtaatgaa aaaagaaatc 1980tgcaatgcgt acactgaact
taacgacccg atgcgtcaac gtcagctgtt tgaagaacag 2040gctaaagcta
aggcggcggg tgatgacgaa gccatgttca tcgatgaaaa cttctgcacc
2100gctctggagt atggtctgcc tccgaccgct ggttggggta tgggtattga
ccgtgtggct 2160atgttcctga ctgactctaa caacatcaaa gaagttctgc
tgttccctgc tatgaaacct 2220gaagacaaaa aagaaaacgt agcgaccact
gacacccttg aatctaccac tgtaggtact 2280agcgtagcgg gtcaccatca
ccaccatcac 2310
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References