U.S. patent application number 11/538619 was filed with the patent office on 2009-10-22 for ubiquitin ligase assay.
Invention is credited to Jianing Huang, Sarkiz D. Issakani, Todd R. Pray, Julie Sheung.
Application Number | 20090263831 11/538619 |
Document ID | / |
Family ID | 24164065 |
Filed Date | 2009-10-22 |
United States Patent
Application |
20090263831 |
Kind Code |
A1 |
Issakani; Sarkiz D. ; et
al. |
October 22, 2009 |
UBIQUITIN LIGASE ASSAY
Abstract
The invention relates to assays for measuring ubiquitin ligase
activity and for identifying modulators of ubiquitin ligase
enzymes.
Inventors: |
Issakani; Sarkiz D.; (San
Jose, CA) ; Huang; Jianing; (Foster City, CA)
; Sheung; Julie; (San Francisco, CA) ; Pray; Todd
R.; (San Francisco, CA) |
Correspondence
Address: |
Klarquist Sparkman, LLP
121 SW Salmon St, Suite 1600
Portland
OR
97204
US
|
Family ID: |
24164065 |
Appl. No.: |
11/538619 |
Filed: |
October 4, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11328747 |
Jan 9, 2006 |
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11538619 |
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10835096 |
Apr 28, 2004 |
7022493 |
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11328747 |
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09826312 |
Apr 3, 2001 |
6737244 |
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10835096 |
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09542497 |
Apr 3, 2000 |
6740495 |
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09826312 |
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Current U.S.
Class: |
435/7.8 |
Current CPC
Class: |
Y10S 436/805 20130101;
G01N 33/573 20130101; G01N 33/582 20130101; C12Q 1/25 20130101;
G01N 2500/00 20130101; C12Q 1/37 20130101; G01N 2333/9015
20130101 |
Class at
Publication: |
435/7.8 |
International
Class: |
G01N 33/53 20060101
G01N033/53 |
Claims
1. A method of assaying ubiquitin ligase activity comprising: a)
combining: i) tag1-ubiquitin, wherein the ubiquitin has at least
95% sequence identity to an amino acid sequence depicted in an
accession number selected from the group consisting of P02248,
AAA36788 and AAB06013 or is encoded by a nucleotide sequence having
at least 95% sequence identity to a nucleotide sequence depicted in
an accession number selected from the group consisting of M26880,
AB003730 and U49869; ii) ubiquitin activating enzyme (E1); iii)
ubiquitin conjugating enzyme (E2); iv) tag2-ubiquitin ligase (E3);
b) measuring the amount of said tag1-ubiquitin bound to said
ubiquitin ligase (E3), whereby the amount of said tag1-ubiquitin
bound to said ubiquitin ligase (E3) indicates said ubiquitin ligase
activity.
2. The method of claim 1, further comprising: a) combining: v) a
candidate ubiquitin ligase modulator.
3. The method of claim 1, wherein the ubiquitin activating enzyme
(E1) has at least 95% sequence identity to an amino acid sequence
depicted in an accession number selected from the group consisting
of A38564, S23770, AAA61246, P22314, CAA40296 and BAA33144.
4. The method of claim 1, wherein the ubiquitin activating enzyme
(E1) is encoded by a nucleotide sequence having at least 95%
sequence identity to a nucleotide sequence depicted in an accession
number selected from the group consisting of M58028, X56976 and
AB012190.
5. The method of claim 1, wherein ubiquitin conjugating enzyme (E2)
is selected from the group consisting of Ubiquitin conjugating
enzyme 5 (Ubc5), Ubiquitin conjugating enzyme 3 (Ubc3), Ubiquitin
conjugating enzyme 4 (Ubc4), and Ubiquitin conjugating enzyme X
(UbcX).
6. The method of claim 1, wherein ubiquitin conjugating enzyme (E2)
has at least 95% sequence identity to an amino acid sequence
depicted in an accession number selected from the group consisting
of AAC37534, P49427, CAA82525, AAA58466, AAC41750, P51669,
AAA91460, AAA91461, CAA63538, AAC50633, P27924, AAB36017, Q16763,
AAB86433, AAC26141, CAA04156, BAA11675, Q16781, NP.sub.--003333,
BAB18652, AAH00468, CAC16955, CAB76865, CAB76864, O00762,
XP.sub.--009804, XP.sub.--009488, XP.sub.--006823, XP.sub.--006343,
XP.sub.--005934, XP.sub.--002869, XP.sub.--003400, XP.sub.--009365,
XP.sub.--010361, XP.sub.--004699, XP.sub.--004019, O14933, P50550,
P52485, P51668, P51669, P49459, P37286, P23567, P56554, CAB45853,
NP.sub.--003331, NP.sub.--003330, NP.sub.--003329, AAB53362 and
NP.sub.--008950.
7. The method of claim 1, wherein the ubiquitin conjugating enzyme
(E2) is encoded by a nucleotide sequence having at least 95%
sequence identity to a nucleotide sequence depicted in an accession
number selected from the group consisting of Z29328, L40146,
U39317, U39318, X92962, U58522, S81003, AF031141, AF075599,
AJ000519, XM.sub.--009488, NM.sub.--007019, U73379 and D83004.
8. The method of claim 1, wherein tag2-ubiquitin ligase (E3)
comprises a RING finger protein.
9. The method of claim 8, wherein said RING finger protein is
selected from the group consisting of Regulator of cullins 1
(ROC1), Regulator of cullins 2 (ROC2), and Anaphase Promoting
complex 11 (APC11).
10. The method of claim 8, wherein said RING finger protein has at
least 95% sequence identity to an amino acid sequence depicted in
an accession number selected from the group consisting of AAD30147,
AAD30146, and 6320196.
11. The method of claim 8, wherein said RING finger protein is
encoded by a nucleotide sequence having at least 95% sequence
identity to a nucleotide sequence depicted in an accession number
selected from the group consisting of AF142059, AF142060 and
nucleic acids 433493 to 433990 of NC.sub.--001136.
12. The method of claim 1, wherein tag2-ubiquitin ligase (E3)
comprises a Cullin.
13. The method of claim 12, wherein said Cullin is selected from
the group consisting of Cullin 1 (CUL1), Cullin 2 (CUL2), Cullin 3
(CUL3), Cullin 4A (CUL4A), Cullin 4B (CUL4B), Cullin 5 (CUL5), and
Anaphase Promoting complex 2 (APC2).
14. The method of claim 12, wherein said Cullin has at least 95%
sequence identity to an amino acid sequence depicted in an
accession number selected from the group consisting of 4503161,
AAC50544, AAC36681, 4503163, AAC51190, AAD23581, 4503165, AAC36304,
AAC36682, AAD45191, AAC50548, Q13620, 4503167 and AAF05751.
15. The method of claim 12, wherein said Cullin is encoded by a
nucleotide sequence having at least 95% sequence identity to a
nucleotide sequence depicted in an accession number selected from
the group consisting of NM.sub.--003592, U58087, AF062536,
AF126404, NM.sub.--003591, U83410, NM.sub.--003590, AF062537,
AF064087, AF077188, U58091, NM.sub.--003478, X81882 and
AF191337.
16. The method of claim 1, wherein tag2-ubiquitin ligase (E3)
comprises a RING finger protein/Cullin combination.
17. The method of claim 16, wherein said RING finger protein/Cullin
combination is selected from the group consisting of Anaphase
promoting complex 2 (APC2)/Anaphase Promoting complex 11 (APC11),
Regulator of cullins 1 (ROC1)/Cullin 1 (CUL1), Regulator of cullins
1 (ROC1)/Cullin 2 (CUL2), and Regulator of cullins 2(ROC2)/Cullin 5
(CUL5).
18. The method of claim 1, wherein said tag1 is a label or a
partner of a binding pair.
19. The method of claim 18, wherein said label is a fluorescent
label.
20. The method of claim 19, wherein said measuring is by measuring
luminescence.
21. The method of claim 18, wherein said partner of a binding pair
is selected from the group consisting of an antigen, biotin, and
calmodalin binding protein (CBP).
22. The method of claim 21, wherein said partner of a binding pair
is labeled by indirect labeling.
23. The method of claim 22, wherein said indirect labeling is with
a fluorescent label or a label enzyme.
24. The method of claim 23, wherein said measuring is by measuring
luminescence.
25. The method of claim 23, wherein said label enzyme is selected
from the group consisting of horseradish peroxidase, alkaline
phosphatase and glucose oxidase.
26. The method of claim 25, wherein said label enzyme is reacted
with a label enzyme substrate which produces a fluorescent
product.
27. The method of claim 26, wherein said measuring is by measuring
luminescence.
28. The method of claim 27, wherein said tag1 is FLAG (DYKDDDDK;
SEQ ID NO: 16).
29. The method of claim 23, wherein said partner of a binding pair
is FLAG and said indirect labeling is via anti-FLAG (DYKDDDDK; SEQ
ID NO: 16).
30. The method of claim 22, wherein said partner of a binding pair
is FLAG (DYKDDDDK; SEQ ID NO: 16).
31. The method of claim 21, wherein said antigen is FLAG (DYKDDDDK;
SEQ ID NO: 16).
32. The method of claim 18, wherein said tag2 is a surface
substrate binding molecule.
33. The method of claim 32, wherein said surface substrate binding
molecule is a polyhistidine structure (His-tag).
34. The method of claim 33, wherein said assaying is performed in a
multi-well plate comprising a surface substrate comprising nickel.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 11/328,747, filed Jan. 9, 2006, which is a is a continuation of
U.S. application Ser. No. 10/835,096, filed Apr. 28, 2004, now U.S.
Pat. No. 7,022,493, which is a continuation of U.S. application
Ser. No. 09/826,312, filed Apr. 3, 2001, now U.S. Pat. No.
6,737,244, which is a continuation-in-part of U.S. application Ser.
No. 09/542,497, filed Apr. 3, 2000, now U.S. Pat. No. 6,740,495,
all of which are hereby incorporated herein by reference for all
purposes.
FIELD OF THE INVENTION
[0002] This invention is directed to assays for measuring the
activity of ubiquitination enzymes. The invention is also directed
to assays for identifying modulators of ubiquitination.
BACKGROUND OF THE INVENTION
[0003] Ubiquitin is a highly conserved 76 amino acid protein
expressed in all eukaryotic cells. The levels of many intracellular
proteins are regulated by a ubiquitin-dependent proteolytic
process. This process involves the covalent ligation of ubiquitin
to a target protein, resulting in a poly-ubiquitinated target
protein which is rapidly detected and degraded by the 26S
proteasome.
[0004] The ubiquitination of these proteins is mediated by a
cascade of enzymatic activity. Ubiquitin is first activated in an
ATP-dependent manner by a ubiquitin activating enzyme (E1). The
C-terminus of a ubiquitin forms a high energy thiolester bond with
E1. The ubiquitin is then passed to a ubiquitin conjugating enzyme
(E2; also called ubiquitin carrier protein), also linked to this
second enzyme via a thiolester bond. The ubiquitin is finally
linked to its target protein to form a terminal isopeptide bond
under the guidance of a ubiquitin ligase (E3). In this process,
chains of ubiquitin are formed on the target protein, each
covalently ligated to the next through the activity of E3.
[0005] The components of the ubiquitin ligation cascade have
received considerable attention (for a review, see Weissman, Nature
Reviews 2:169-178 (2001)). E1 and E2 are structurally related and
well characterized enzymes. There are several species of E2 (at
least 25 in mammals), some of which act in preferred pairs with
specific E3 enzymes to confer specificity for different target
proteins. While the nomenclature for E2 is not standardized across
species, investigators in the field have addressed this issue and
the skilled artisan can readily identify various E2 proteins, as
well as species homologues (See Haas and Siepmann, FASEB J. 11:
1257-1268 (1997)).
[0006] E3 enzymes contain two separate activities: a ubiquitin
ligase activity to conjugate ubiquitin to substrates and form
polyubiquitin chains via isopeptide bonds, and a targeting activity
to physically bring the ligase and substrate together. Substrate
specificity of different E3 enzymes is the major determinant in the
selectivity of the ubiquitin-dependent protein degradation
process.
[0007] Some E3 ubiquitin ligases are known to have a single subunit
responsible for the ligase activity. Such E3 ligases that have been
characterized include the HECT (homologous to E6-AP carboxy
terminus) domain proteins, represented by the mammalian E6AP-E6
complex which functions as a ubiquitin ligase for the tumor
suppressor p 53 and which is activated by papillomavirus in
cervical cancer (Huang et al., Science 286:1321-26 (1999)). Single
subunit ubiquitin ligases having a RING domain include Mdm2, which
has also been shown to act as a ubiquitin ligase for p 53, as well
as Mdm2 itself. Other RING domain, single subunit E3 ligases
include: TRAF6, involved in IKK activation; Cbl, which targets
insulin and EGF; Sina/Siah, which targets DCC; Itchy, which is
involved in haematopoesis (B, T and mast cells); and IAP, involved
with inhibitors of apoptosis.
[0008] The best characterized E3 ligase is the APC (anaphase
promoting complex), which is a multi-subunit complex that is
required for both entry into anaphase as well as exit from mitosis
(see King et al., Science 274:1652-59 (1996) for review). The APC
plays a crucial role in regulating the passage of cells through
anaphase by promoting ubiquitin-dependent proteolysis of many
proteins. In addition to degrading the mitotic B-type cyclin for
inactivation of CDC2 kinase activity, the APC is also required for
degradation of other proteins for sister chromatid separation and
spindle disassambly. Most proteins known to be degraded by the APC
contain a conserved nine amino acid motif known as the "destruction
box" that targets them for ubiquitination and subsequent
degradation. However, proteins that are degraded during G1,
including G1 cyclins, CDK inhibitors, transcription factors and
signaling intermediates, do not contain this conserved amino acid
motif. Instead substrate phosphorylation appears to play an
important role in targeting their interaction with an E3 ligase for
ubiquitination (see Hershko et al., Ann. Rev. Biochem. 67:429-75
(1998)).
[0009] In eukaryotes, a family of complexes with E3 ligase activity
play an important role in regulating G1 progression. These
complexes, called SCF's, consist of at least three subunits, SKP1,
Cullins (having at least seven family members) and an F-box protein
(of which hundreds of species are known) which bind directly to and
recruit the substrate to the E3 complex. The combinatorial
interactions between the SCF's and a recently discovered family of
RING finger proteins, the ROC/APC 11 proteins, have been shown to
be the key elements conferring ligase activity to E3 protein
complexes. Particular ROC/Cullin combinations can regulate specific
cellular pathways, as exemplified by the function of APC11-APC2,
involved in the proteolytic control of sister chromatid separation
and exit from telophase into G1 in mitosis (see King et al., supra;
Koepp et al., Cell 97:431-34 (1999)), and ROC1-Cullin 1, involved
in the proteolytic degradation of I.sub..kappa.B.sub..alpha., in
NF-.sub..kappa.B/I.sub..kappa.B mediated transcription regulation
(Tan et al., Mol. Cell. 3(4):527-533 (1999); Laney et al., Cell
97:427-30 (1999)).
[0010] Because the E3 complex is the major determinant of selection
for protein degradation by the ubiquitin-dependent proteolytic
process, modulators of E3 ligase activity may be used to upregulate
or downregulate specific molecules involved in cellular signal
transduction. Disease processes can be treated by such up- or down
regulation of signal transducers to enhance or dampen specific
cellular responses. This principle has been used in the design of a
number of therapeutics, including Phosphodiesterase inhibitors for
airway disease and vascular insufficiency, Kinase inhibitors for
malignant transformation and Proteasome inhibitors for inflammatory
conditions such as arthritis.
[0011] Due to the importance of ubiquitination in cellular
regulation and the wide array of different possible components in
ubiquitin-dependent proteolysis, there is a need for a fast and
simple means for assaying E3 ligase activity. Furthermore, such an
assay would be very useful for the identification of modulators of
E3 ligase. Accordingly, it is an object of the present invention to
provide methods of assaying ubiquitin ligase activity, which
methods may further be used to identify modulators of ubiquitin
ligase activity.
DESCRIPTION OF THE RELATED ART
[0012] Tan et al., supra, disclose that ROC1/Cul 1 catalyzes
ubiquitin polymerization in the absence of target protein
substrate. Ohta et al., Mol. Cell. 3(4):535 541 (1999) disclose
that APC11/APC2 also catalyze ubiquitin polymerization in the
absence of target protein substrate, and that this activity is
dependent on the inclusion of the proper E2 species. Rolfe et al.,
U.S. Pat. No. 5,968,761 disclose an assay for identifying
inhibitors of ubiquitination of a target regulatory protein.
SUMMARY OF THE INVENTION
[0013] The present invention provides methods for assaying
ubiquitin ligase activity and screening for agents which modulate
ubiquitin ligase activity. In one aspect, a method of assaying
ubiquitin ligase activity is provided involving the steps of
combining ubiquitin, E1, E2 and E3 and measuring the amount of
ubiquitin bound to E3. This method may further involve combining a
candidate ubiquitin ligase modulator in the combining step. This
method does not require a specific target protein to be
ubiquitinated. In a preferred embodiment, a substrate protein for
ubiquitination other than ubiquitin itself is specifically
excluded.
[0014] In one embodiment of the assay described above, ubiquitin is
in the form of tag1-ubiquitin. In another embodiment, E3 is in the
form of tag2-E3. In these embodiments tag1 may be a label or a
partner of a binding pair. In one embodiment, tag1 is a fluorescent
label, in which case measuring the amount of ubiquitin bound to E3
may be by measuring luminescence.
[0015] In another embodiment, tag1 is a member of a binding pair
chosen from the group antigen, biotin and CBP. In this latter
embodiment, the partner of a binding pair may be labeled by
indirect labeling, which may be by a fluorescent label or a label
enzyme. The label enzyme may be horseradish peroxidase, alkaline
phosphatase or glucose oxidase. When the indirect labeling is by a
fluorescent label, measuring the amount of ubiquitin bound to E3
may be by measuring luminescence. In the case that the indirect
labeling is by a label enzyme, said enzyme may be reacted with a
substrate which produces a fluorescent product, in which case,
measuring the amount of ubiquitin bound to E3 may be by measuring
luminescence. In one embodiment of the method above, tag1 is a FLAG
antigen. In this embodiment, indirect labeling may be by
anti-FLAG.
[0016] In one aspect of the above method, tag2 is a surface binding
molecule, which may be His-tag. In this latter case, the assaying
may be performed in a multi-well plate comprising a surface
substrate comprising nickel.
[0017] In a different embodiment of the method above, when tag1 is
a fluorescent label, the combining step further includes combining
tag3-ubiquitin. Tag3 may be the second member of a FRET pair with
tag1 or it may be a quencher of tag1. In this embodiment, measuring
the amount of ubiquitin bound to E3 may be by measuring fluorescent
emission, which may involve measuring the fluorescent emission
spectrum. In this last embodiment, the method may further comprise
comparing the measured fluorescent emission spectrum with the
fluorescent emission spectrum of unbound tag1- and tag3-ubiquitin.
When measuring the amount of ubiquitin bound to E3 is by measuring
the fluorescent emission spectrum, this measuring may be continuous
or at specific time points following the original combining of
materials.
[0018] In another aspect of the invention, a method of identifying
modulators of ubiquitination enzymes is provided. This method
involves combining tag1-ubiquitin, a candidate modulator, E1, E2
and tag2-E3 and measuring the amount of tag1-ubiquitin bound to
tag2-E3. In another embodiment, this method further comprises
combining tag1-ubiquitin, a candidate modulator, E1 and tag2-E2 and
measuring the amount of tag1-ubiquitin bound to the tag2-E2. In a
preferred embodiment, target protein (i.e., a substrate protein
other than ubiquitin itself) is specifically excluded in the
method.
[0019] In the embodiments of the method of identifying modulators
of ubiquitination enzymes, tag1 may be a label or a partner of a
binding pair. If tag1 is a label, it may be a fluorescent label, in
which case, measuring the amount of bound tag1-ubiquitin may be by
measuring luminescence. If tag1 is a partner of a binding pair, the
potential binding pair partners, labeling options and subsequent
measuring options are substantially as described for tag1 above for
the method of assaying ubiquitin ligase activity.
[0020] In the above method of identifying modulators of
ubiquitination enzymes, tag2 and tag3 may be surface substrate
binding molecules. Options for such molecules and conditions for
performing the method are as described for the method of assaying
ubiquitin ligase activity.
[0021] In another aspect of the invention, a method of assaying
ubiquitination enzyme activity is provided. This method comprises
combining tag1-ubiquitin and tag2-ubiquitin, E1, E2 and E3 under
conditions in which ubiquitination can take place and measuring the
amount or rate of ubiquitination. In this embodiment, tag1 and tag2
constitute a FRET pair or tag1 is a fluorescent label and tag2 is a
quencher of tag1. In one embodiment, the method includes combining
a candidate ubiquitination modulator with the other components. In
a preferred embodiment of this method, measuring is by measuring
the fluorescent emission spectrum from the combination, preferably
continuously or at specific time points following combining the
components. These measurements may be compared to the fluorescent
emission spectrum of unbound tag1 and tag2 ubiquitin.
[0022] Also provided herein is a method of identifying a
ubiquitination modulator. This method involved combining a
candidate ubiquitination modulator, tag1-ubiquitin and
tag2-ubiquitin, E1, E2 and E3 under conditions in which
ubiquitination can take place and measuring the amount or rate of
ubiquitination. In this embodiment, tag1 and tag2 constitute a FRET
pair or tag1 is a fluorescent label and tag2 is a quencher of tag1.
In one embodiment, the method includes combining a candidate
ubiquitination modulator with the other components. In a preferred
embodiment of this method, measuring is by measuring the
fluorescent emission spectrum from the combination, preferably
continuously or at specific time points following combining the
components. These measurements may be compared to the fluorescent
emission spectrum of unbound tag1 and tag2 ubiquitin.
[0023] In the latter two assays described, the ubiquitin may be in
the form tag1,3-ubiquitin and tag2,3-ubiquitin, wherein tag3 is a
member of a binding pair, preferably FLAG. In another embodiment of
these assays, E3 may be in the form of tag4-E3, wherein tag4 is a
surface substrate bonding molecule.
[0024] In still another aspect of the invention, compositions are
provided for use in assaying ubiquitination. The composition
comprises tag1-ubiquitin and tag2-ubiquitin, wherein tag1 and tag2
constitute a FRET pair or tag1 is a fluorescent label and tag2 is a
quencher of tag1. In one embodiment, the composition further
comprises E1, E2 and E3. In a preferred embodiment, the composition
further comprises a candidate ubiquitination modulator. In yet
another embodiment, the composition comprises a target protein.
[0025] In addition, provided herein are compositions for use in
assaying for a ubiquitination modulator. The composition comprises
a candidate ubiquitination modulator, tag1-ubiquitin and
tag2-ubiquitin, wherein tag1 and tag2 constitute a FRET pair or
tag1 is a fluorescent label and tag2 is a quencher of tag1. In one
embodiment, the composition further comprises E1, E2 and E3. In one
embodiment, the composition comprises a target protein.
[0026] In preferred embodiments of the assays and compositions
described above, E2 is selected from the group consisting of Ubc5,
Ubc3, Ubc4 and UbcX. In a preferred embodiment, E3 comprises a RING
finger protein, preferably selected from the group consisting of
ROC1, ROC2 and APC 11. In a preferred embodiment, E3 comprises a
Cullin, preferably selected from the group consisting of CUL1,
CUL2, CUL3, CUL4A, CUL4B, CUL5 and APC2. In a preferred embodiment,
E3 comprises a RING finger protein/Cullin combination, preferably
selected from the group consisting of APC11/APC2, ROC1/CUL1,
ROC1/CUL2 and ROC2/CUL5.
[0027] Other aspects of the invention will become apparent to the
skilled artisan from the following description of the
invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0028] FIG. 1 shows the relative amounts of fluorescently labeled
ubiquitin in a ubiquitin activating and conjugating assay. In these
experiments, E2 is His-Ubch5c.
[0029] FIG. 2 shows the relative amounts of ubiquitin ligase
activity resulting from various combinations of ubiquitination
enzymes. In these experiments, E3 comprises the RING finger protein
ROC1 and the Cullin Cul1.
[0030] FIG. 3 shows relative ubiquitin ligase activity in an assay
combining ubiquitin, E1, E2 and E3. FIG. 3A shows relative
ubiquitin ligase activity using varying amounts of E1 in the
presence and absence of DMSO. FIG. 3B shows relative ubiquitin
ligase activity using varying amounts of ubiquitin and E3.
[0031] FIG. 4 shows the signal to noise ratio of fluorescent label
in a ubiquitin ligase activity assay utilizing FLAG-ubiquitin (SEQ
ID NO: 14) and an anti-FLAG (DYKDDDDK; SEQ ID NO: 16)/anti-mouse
antibody conjugated to HRP and Luminol fluorescent HRP substrate.
The signal was measured from a reaction composition comprising E1,
E2 and E3, which E3 specifically bound the reaction receptacle
surface substrate. The background was measured as the amount of
fluorescence present after performing the assay in the absence of
E3
[0032] FIG. 5 shows the concentration-dependent effect of two
ubiquitin ligase activity modulators in assays measuring ubiquitin
ligase activity with two different E3 enzymes. FIG. 5A shows a
concentration-dependent reduction in ubiquitin ligase activity in
assays comprising either ROC1/Cul1 or ROC2/Cul5 as the components
of the E3 ubiquitin ligase. FIG. 5B shows a slightly different
pattern of concentration-dependent reduction of ubiquitin ligase
activity for another modulator.
[0033] FIG. 6 shows the proportions of ubiquitin ligase activity
and ubiquitin conjugating activity in the presence and absence of
two candidate ubiquitin ligase enzyme modulators for combinations
of E1, E2 and E3 and combinations of enzymes E1 and E2. FIG. 6A
shows a candidate ubiquitination enzyme modulator that affects only
E3. FIG. 6B shows candidate ubiquitination enzyme modulator that
affects enzymes other than E3.
[0034] FIG. 7 shows the concentration dependent effects of two
candidate ubiquitin ligase modulators on ubiquitin ligase activity
and ubiquitin conjugating activity. FIG. 7A shows the results for a
candidate modulator having a concentration dependent effect on
ubiquitin ligase activity (E1+E2+E3), but not have on ubiquitin
conjugating activity (E1+E2), thus affecting only the E3 ligase.
FIG. 7B shows the results for a candidate modulator having a
concentration-dependent effect on both ubiquitin conjugating
activity and ubiquitin ligase activity, thus affecting a component
other than the E3 ligase.
[0035] FIGS. 8A and 8B show the nucleic acid sequence encoding
rabbit E1 and the amino acid sequence of rabbit E1,
respectively.
[0036] FIGS. 9A and 9B show the nucleic acid sequence encoding the
E2 Ubc5c and the amino acid sequence of the E2 Ubc5c,
respectively.
[0037] FIG. 10 shows the amino acid sequence of the RING finger
protein APC11.
[0038] FIG. 11 shows the amino acid sequence of the RING finger
protein ROC1.
[0039] FIGS. 12A and 12B show the nucleic acid sequence encoding
the RING finger protein ROC2 and the amino acid sequence of ROC2,
respectively.
[0040] FIGS. 13A and 13B show the nucleic acid sequence encoding
the Cullin CUL5 and the amino acid sequence of CUL5,
respectively.
[0041] FIGS. 14A and 14B show the nucleic acid sequence encoding
the Cullin APC2 and the amino acid sequence of APC2,
respectively.
[0042] FIGS. 15A, 15B and 15C (SEQ ID NOS: 13-15) show the amino
acid sequences of human ubiquitin, FLAG-ubiquitin and
FLAG-Cys-ubiquitin, respectively. The FLAG (DYKDDDDK; SEQ ID NO:
16) and FLAG-Cys (SEQ ID NO: 17) portions of the sequence are shown
in bold.
[0043] FIGS. 16A and 16B show the E3 ligase dependent incorporation
of FLAG-Ala-Cys-ubiquitin (SEQ ID NO: 18) labeled with FRET
fluorophores into E3-ubiquitin complex. Isolation by HPLC shows
emissions from free ubiquitin and ubiquitin attached to the E3
ligase. The traces show fluorescent emission at the wavelength
described below, under excitation at 336 nm, the optimal excitation
wavelength for IAEDANS. FIG. 16A shows the fluorescence signals of
IAEDANS (490 nm; larger peak) and fluorescein (515 nm; smaller
peak) labeled ubiquitin following combination with E1 and E2 only.
The free ubiquitin was isolated using high performance liquid
chromatography (HPLC). FIG. 16B shows the fluorescence signals of
IAEDANS (490 nm; larger peak at each elution volume) and
fluorescein (515 nm; smaller peak at each elution volume) labeled
ubiquitin following combination with E1 and E2 and E3 (Roc1/Cul1).
The dashed line shows optical density of the protein solution
(scale on right), revealing the high sensitivity of the
fluorophores despite a very low concentration of protein.
[0044] FIG. 17 shows the fluorescence emission spectra of free
ubiquitin labeled with the FRET donor/acceptor pair MANS and
fluorescein under excitation at 336 nm. The dashed line shows the
emission spectra of free labeled ubiquitin (reactants), while the
solid line shows the emission spectra of labeled ubiquitin bound to
E3 (products). The greatly increased 515:490 nm emission ratio of
the E3 bound ubiquitin as compared with the free ubiquitin shows
the energy transfer from the EDANS donor to the fluorescein
acceptor of this FRET donor/acceptor pair.
DETAILED DESCRIPTION OF THE INVENTION
[0045] The present invention is directed to methods for assaying
ubiquitin ligase activity. In a broad embodiment, the method
provides measuring ubiquitin ligase activity directly where the
reaction has occurred, thus obviating the need for target proteins
and subsequent analysis such as separating ligated from unligated
material in an SDS PAGE procedure. This allows multi-well array
analysis and high throughput screening techniques for modulators of
ubiquitination activity. In addition, the present methods allow the
analysis of many different combinations of E3 components and E2/E3
combinations, without requiring prior identification of specific
target substrates.
[0046] In general, the method involves combining ubiquitin and
ubiquitin ligation enzymes and measuring the amount of ubiquitin
ligated to a ubiquitination substrate protein. In a preferred
embodiment, the ubiquitination substrate protein is ubiquitin
itself, and what is measured is poly-ubiquitin chains produced in
the ligase reaction. Therefore, as used herein, "ubiquitination
substrate protein" means a protein to which ubiquitin is bound
through the activity of ubiquitination enzymes and "ubiquitination"
and grammatical equivalents thereof means the binding of ubiquitin
to a substrate protein.
[0047] In a preferred embodiment, no specific target protein is
used to measure ubiquitin ligase activity. By "target protein"
herein is meant a protein other than ubiquitin to which ubiquitin
is ligated by ubiquitination enzymes. In this embodiment,
preferably, the polyubiquitin chains measured are bound to E3. In
another preferred embodiment, the polyubiquitin chains measured may
be bound to E3 or not.
[0048] In a preferred embodiment, E3 is attached to the surface of
a reaction vessel, such as the well of a multi-well plate. This
embodiment facilitates the separation of ligated ubiquitin from
unligated ubiquitin. Means of attaching E3 to the surface of a
reaction vessel are described below. This embodiment allows the
ubiquitin ligase reaction and detection and measurement of ligated
ubiquitin to occur in the same vessel, making the assay useful for
high throughput screening applications.
[0049] In another preferred embodiment, E3 is free in solution. In
this embodiment, ubiquitination activity is monitored using a
system that produces a signal which varies with the extent of
ubiquitination, such as the fluorescence resonance energy transfer
(FRET) system described in detail below.
[0050] In a preferred embodiment, the ubiquitin is labeled, either
directly or indirectly, as further described below, and the amount
of label is measured. This allows for easy and rapid detection and
measurement of ligated ubiquitin, making the assay useful for
high-throughput screening applications. In one preferred
embodiment, the signal of the label varies with the extent of
ubiquitination, such as in the FRET system described below. One of
ordinary skill in the art will recognize the applicability of the
present invention to screening for agents which modulate
ubiquitination.
[0051] Accordingly, the present invention provides methods and
compositions for assaying ubiquitin ligase activity. By "ubiquitin"
herein is meant a polypeptide which is ligated to another
polypeptide by ubiquitin ligase enzymes. The ubiquitin can be from
any species of organism, preferably a eukaryotic species.
Preferably, the ubiquitin is mammalian. More preferably, the
ubiquitin is human ubiquitin. In a most preferred embodiment, the
ubiquitin has the amino acid sequence depicted in FIG. 15A.
[0052] In a preferred embodiment, when ubiquitin is ligated to a
target protein, that protein is targeted for degradation by the 26S
proteasome.
[0053] Preferred embodiments of the invention utilize a 76 amino
acid human ubiquitin. Other embodiments utilize variants of
ubiquitin, as further described below.
[0054] Also encompassed by "ubiquitin" is naturally occurring
alleles and man-made variants of such a 76 amino acid polypeptide.
In a preferred embodiment, the ubiquitin has the amino acid
sequence of that depicted in ATCC accession number P02248,
incorporated herein by reference. ATCC accession numbers are found
in Genbank. Sequences of GenBank accession numbers are incorporated
herein by reference. GenBank is known in the art, see, e.g.,
Benson, DA, et al., Nucleic Acids Research 26:1-7 (1998) and
http://www.ncbi.nlm.nih.gov/. Preferably, the ubiquitin has the
amino acid sequence depicted in FIG. 15A. In a preferred
embodiment, variants of ubiquitin have an overall amino acid
sequence identity of preferably greater than about 75%, more
preferably greater than about 80%, even more preferably greater
than about 85% and most preferably greater than 90% of the amino
acid sequence depicted in FIG. 15A. In some embodiments the
sequence identity will be as high as about 93 to 95 or 98%.
[0055] In another preferred embodiment, a ubiquitin protein has an
overall sequence similarity with the amino acid sequence depicted
in FIG. 15A of greater than about 80%, more preferably greater than
about 85%, even more preferably greater than about 90% and most
preferably greater than 93%. In some embodiments the sequence
identity will be as high as about 95 to 98 or 99%.
[0056] Preferred embodiments of the invention utilize a 76 amino
acid human ubiquitin. Other embodiments utilize variants of
ubiquitin, as further described below.
[0057] Also encompassed by "ubiquitin" is naturally occurring
alleles and man-made variants of such a 76 amino acid polypeptide.
In a preferred embodiment, the ubiquitin has the amino acid
sequence of amino acids 1-76 of ATCC accession number AAA36789 or
AAB06013, incorporated herein by reference. In a preferred
embodiment, variants of ubiquitin have an overall amino acid
sequence identity of preferably greater than about 75%, more
preferably greater than about 80%, even more preferably greater
than about 85% and most preferably greater than 90% of the amino
acid sequence of amino acids 1-76 of ATCC accession number AAA36789
or AAB06013. In some embodiments the sequence identity will be as
high as about 93 to 95 or 98%.
[0058] In another preferred embodiment, a ubiquitin protein has an
overall sequence similarity with the amino acid sequence of amino
acids 1-76 of ATCC accession number AAA36789 or AAB06013 of greater
than about 80%, more preferably greater than about 85%, even more
preferably greater than about 90% and most preferably greater than
93%. In some embodiments the sequence identity will be as high as
about 95 to 98 or 99%.
[0059] As is known in the art, a number of different programs can
be used to identify whether a protein (or nucleic acid as discussed
below) has sequence identity or similarity to a known sequence.
Sequence identity and/or similarity is determined using standard
techniques known in the art, including, but not limited to, the
local sequence identity algorithm of Smith & Waterman, Adv.
Appl. Math. 2:482 (1981), by the sequence identity alignment
algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),
by the search for similarity method of Pearson & Lipman, PNAS
USA 85:2444 (1988), by computerized implementations of these
algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin
Genetics Software Package, Genetics Computer Group, 575 Science
Drive, Madison, Wis.), the Best Fit sequence program described by
Devereux et al., Nucl. Acid Res. 12:387-395 (1984), preferably
using the default settings, or by inspection. Preferably, percent
identity is calculated by FastDB based upon the following
parameters: mismatch penalty of 1; gap penalty of 1; gap size
penalty of 0.33; and joining penalty of 30, "Current Methods in
Sequence Comparison and Analysis," Macromolecule Sequencing and
Synthesis, Selected Methods and Applications, pp 127-149 (1988),
Alan R. Liss, Inc.
[0060] An example of a useful algorithm is PILEUP. PILEUP creates a
multiple sequence alignment from a group of related sequences using
progressive, pairwise alignments. It can also plot a tree showing
the clustering relationships used to create the alignment. PILEUP
uses a simplification of the progressive alignment method of Feng
& Doolittle, J. Mol. Evol. 35:351-360 (1987); the method is
similar to that described by Higgins & Sharp CABIOS 5:151-153
(1989). Useful PILEUP parameters including a default gap weight of
3.00, a default gap length weight of 0.10, and weighted end
gaps.
[0061] Another example of a useful algorithm is the BLAST
algorithm, described in Altschul et al., J. Mol. Biol. 215,
403-410, (1990) and Karlin et al., PNAS USA 90:5873-5787 (1993). A
particularly useful BLAST program is the WU-BLAST-2 program which
was obtained from Altschul et al., Methods in Enzymology, 266:
460-480 (1996); http://blast.wustl/edu/blast/README.html].
WU-BLAST-2 uses several search parameters, most of which are set to
the default values. The adjustable parameters are set with the
following values: overlap span=1, overlap fraction=0.125, word
threshold (T)=11. The HSP S and HSP S2 parameters are dynamic
values and are established by the program itself depending upon the
composition of the particular sequence and composition of the
particular database against which the sequence of interest is being
searched; however, the values may be adjusted to increase
sensitivity.
[0062] An additional useful algorithm is gapped BLAST as reported
by Altschul et al. Nucleic Acids Res. 25:3389-3402. Gapped BLAST
uses BLOSUM-62 substitution scores; threshold T parameter set to 9;
the two-hit method to trigger ungapped extensions; charges gap
lengths of k a cost of 10+k, X.sub.u set to 16, and X.sub.g set to
40 for database search stage and to 67 for the output stage of the
algorithms. Gapped alignments are triggered by a score
corresponding to .about.22 bits.
[0063] A percent amino acid sequence identity value is determined
by the number of matching identical residues divided by the total
number of residues of the "longer" sequence in the aligned region.
The "longer" sequence is the one having the most actual residues in
the aligned region (gaps introduced by WU-Blast-2 to maximize the
alignment score are ignored).
[0064] The alignment may include the introduction of gaps in the
sequences to be aligned. In addition, for sequences which contain
either more or fewer amino acids than the amino acid sequence
depicted in FIG. 15A, it is understood that in one embodiment, the
percentage of sequence identity will be determined based on the
number of identical amino acids in relation to the total number of
amino acids. Thus, for example, sequence identity of sequences
shorter than that of the sequence depicted in FIG. 15A, as
discussed below, will be determined using the number of amino acids
in the shorter sequence, in one embodiment. In percent identity
calculations relative weight is not assigned to various
manifestations of sequence variation, such as, insertions,
deletions, substitutions, etc.
[0065] In one embodiment, only identities are scored positively
(+1) and all forms of sequence variation including gaps are
assigned a value of "0", which obviates the need for a weighted
scale or parameters as described below for sequence similarity
calculations. Percent sequence identity can be calculated, for
example, by dividing the number of matching identical residues by
the total number of residues of the "shorter" sequence in the
aligned region and multiplying by 100. The "longer" sequence is the
one having the most actual residues in the aligned region.
[0066] Ubiquitin proteins of the present invention may be shorter
or longer than the amino acid sequence depicted in FIG. 15A. Thus,
in a preferred embodiment, included within the definition of
ubiquitin are portions or fragments of the amino acid sequence
depicted in FIG. 15A. In one embodiment herein, fragments of
ubiquitin are considered ubiquitin proteins if they are ligated to
another polypeptide by ubiquitin ligase enzymes.
[0067] In addition, as is more fully outlined below, ubiquitin can
be made longer than the amino acid sequence depicted in FIG. 15A;
for example, by the addition of tags, the addition of other fusion
sequences, or the elucidation of additional coding and non-coding
sequences. As described below, the fusion of a ubiquitin peptide to
a fluorescent peptide, such as Green Fluorescent Peptide (GFP), is
particularly preferred.
[0068] The ubiquitin protein, as well as other proteins of the
present invention, are preferably recombinant. A "recombinant
protein" is a protein made using recombinant techniques, i.e.
through the expression of a recombinant nucleic acid as described
below. In a preferred embodiment, the ubiquitin of the invention is
made through the expression of a nucleic acid as depicted in ATCC
accession number M26880, U49869 or AB003730, or a fragment thereof.
In a most preferred embodiment, the nucleic acid encodes the amino
acid sequence depicted in FIG. 15A. A recombinant protein is
distinguished from naturally occurring protein by at least one or
more characteristics. For example, the protein may be isolated or
purified away from some or all of the proteins and compounds with
which it is normally associated in its wild type host, and thus may
be substantially pure. For example, an isolated protein is
unaccompanied by at least some of the material with which it is
normally associated in its natural state, preferably constituting
at least about 0.5%, more preferably at least about 5% by weight of
the total protein in a given sample. A substantially pure protein
comprises at least about 75% by weight of the total protein, with
at least about 80% being preferred, and at least about 90% being
particularly preferred. The definition includes the production of a
protein from one organism in a different organism or host cell.
Alternatively, the protein may be made at a significantly higher
concentration than is normally seen, through the use of an
inducible promoter or high expression promoter, such that the
protein is made at increased concentration levels. Alternatively,
the protein may be in a form not normally found in nature, as in
the addition of an epitope tag or amino acid substitutions,
insertions and deletions, as discussed below.
[0069] As used herein and further defined below, "nucleic acid" may
refer to either DNA or RNA, or molecules which contain both deoxy-
and ribonucleotides. The nucleic acids include genomic DNA, cDNA
and oligonucleotides including sense and anti-sense nucleic acids.
Such nucleic acids may also contain modifications in the
ribose-phosphate backbone to increase stability and half life of
such molecules in physiological environments.
[0070] The nucleic acid may be double stranded, single stranded, or
contain portions of both double stranded or single stranded
sequence. As will be appreciated by those in the art, the depiction
of a single strand ("Watson") also defines the sequence of the
other strand ("Crick"); thus the sequences depicted in FIGS. 1 and
3 also include the complement of the sequence. By the term
"recombinant nucleic acid" herein is meant nucleic acid, originally
formed in vitro, in general, by the manipulation of nucleic acid by
endonucleases, in a form not normally found in nature. Thus an
isolated nucleic acid, in a linear form, or an expression vector
formed in vitro by ligating DNA molecules that are not normally
joined, are both considered recombinant for the purposes of this
invention. It is understood that once a recombinant nucleic acid is
made and reintroduced into a host cell or organism, it will
replicate non-recombinantly, i.e. using the in vivo cellular
machinery of the host cell rather than in vitro manipulations;
however, such nucleic acids, once produced recombinantly, although
subsequently replicated non-recombinantly, are still considered
recombinant for the purposes of the invention.
[0071] The terms "polypeptide" and "protein" may be used
interchangeably throughout this application and mean at least two
covalently attached amino acids, which includes proteins,
polypeptides, oligopeptides and peptides. The protein may be made
up of naturally occurring amino acids and peptide bonds, or
synthetic peptidomimetic structures. Thus "amino acid", or "peptide
residue", as used herein means both naturally occurring and
synthetic amino acids. For example, homo-phenylalanine, citrulline
and noreleucine are considered amino acids for the purposes of the
invention. "Amino acid" also includes imino acid residues such as
proline and hydroxyproline. The side chains may be in either the
(R) or the (S) configuration. In the preferred embodiment, the
amino acids are in the (S) or L-configuration. If non-naturally
occurring side chains are used, non-amino acid substituents may be
used, for example to prevent or retard in vivo degradation.
[0072] In one embodiment, the present invention provides
compositions containing protein variants, for example ubiquitin,
E1, E2 and/or E3 variants. These variants fall into one or more of
three classes: substitutional, insertional or deletional variants.
These variants ordinarily are prepared by site specific mutagenesis
of nucleotides in the DNA encoding a protein of the present
compositions, using cassette or PCR mutagenesis or other techniques
well known in the art, to produce DNA encoding the variant, and
thereafter expressing the DNA in recombinant cell culture as
outlined above. However, variant protein fragments having up to
about 100-150 residues may be prepared by in vitro synthesis using
established techniques. Amino acid sequence variants are
characterized by the predetermined nature of the variation, a
feature that sets them apart from naturally occurring allelic or
interspecies variation of the protein amino acid sequence. The
variants typically exhibit the same qualitative biological activity
as the naturally occurring analogue, although variants can also be
selected which have modified characteristics as will be more fully
outlined below.
[0073] While the site or region for introducing an amino acid
sequence variation is predetermined, the mutation per se need not
be predetermined. For example, in order to optimize the performance
of a mutation at a given site, random mutagenesis may be conducted
at the target codon or region and the expressed variants screened
for the optimal desired activity. Techniques for making
substitution mutations at predetermined sites in DNA having a known
sequence are well known, for example, M13 primer mutagenesis and
PCR mutagenesis. Rapid production of many variants may be done
using techniques such as the method of gene shuffling, whereby
fragments of similar variants of a nucleotide sequence are allowed
to recombine to produce new variant combinations. Examples of such
techniques are found in U.S. Pat. Nos. 5,605,703; 5,811,238;
5,873,458; 5,830,696; 5,939,250; 5,763,239; 5,965,408; and
5,945,325, each of which is incorporated by reference herein in its
entirety. Screening of the mutants is done using ubiquitin ligase
activity assays of the present invention.
[0074] Amino acid substitutions are typically of single residues;
insertions usually will be on the order of from about 1 to 20 amino
acids, although considerably larger insertions may be tolerated.
Deletions range from about 1 to about 20 residues, although in some
cases deletions may be much larger.
[0075] Substitutions, deletions, insertions or any combination
thereof may be used to arrive at a final derivative. Generally
these changes are done on a few amino acids to minimize the
alteration of the molecule. However, larger changes may be
tolerated in certain circumstances. When small alterations in the
characteristics of the protein are desired, substitutions are
generally made in accordance with the following chart:
TABLE-US-00001 CHART I Original Residue Exemplary Substitutions Ala
Ser Arg Lys Asn Gln, His Asp Glu Cys Ser, Ala Gln Asn Glu Asp Gly
Pro His Asn, Gln Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met
Leu, Ile Phe Met, Leu, Tyr Ser Thr Thr Ser Trp Tyr Tyr Trp, Phe Val
Ile, Leu
[0076] Substantial changes in function or immunological identity
are made by selecting substitutions that are less conservative than
those shown in Chart I. For example, substitutions may be made
which more significantly affect: the structure of the polypeptide
backbone in the area of the alteration, for example the
alpha-helical or beta-sheet structure; the charge or hydrophobicity
of the molecule at the target site; or the bulk of the side chain.
The substitutions which in general are expected to produce the
greatest changes in the polypeptide's properties are those in which
(a) a hydrophilic residue, e.g. seryl or threonyl, is substituted
for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl,
phenylalanyl, valyl or alanyl; (b) a cysteine or proline is
substituted for (or by) any other residue; (c) a residue having an
electropositive side chain, e.g. lysyl, arginyl, or histidyl, is
substituted for (or by) an electronegative residue, e.g. glutamyl
or aspartyl; or (d) a residue having a bulky side chain, e.g.
phenylalanine, is substituted for (or by) one not having a side
chain, e.g. glycine.
[0077] The variants typically exhibit the same qualitative
biological activity and will elicit the same immune response as the
naturally occurring analogue, although variants also are selected
to modify the characteristics of the proteins as needed.
Alternatively, the variant may be designed such that the biological
activity of the protein is altered. For example, glycosylation
sites may be altered or removed.
[0078] Covalent modifications of polypeptides are included within
the scope of this invention. One type of covalent modification
includes reacting targeted amino acid residues of a polypeptide
with an organic derivatizing agent that is capable of reacting with
selected side chains or the N- or C-terminal residues of a
polypeptide. Derivatization with bifunctional agents is useful, for
instance, for crosslinking a protein to a water insoluble support
matrix or surface for use in the method for screening assays, as is
more fully described below. Commonly used crosslinking agents
include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,
-hydroxy-succinimide esters, for example, esters with
4-azidosalicylic acid, homobifunctional imidoesters, including
disuccinimidyl esters such as
3,3'-dithiobis(succinimidyl-propionate), bifunctional maleimides
such as bis-N-maleimido-1,8-octane and agents such as
methyl-3-[(p-azidophenyl)dithio]propioimidate.
[0079] Other modifications include deamidation of glutaminyl and
asparaginyl residues to the corresponding glutamyl and aspartyl
residues, respectively, hydroxylation of proline and lysine,
phosphorylation of hydroxyl groups of seryl or threonyl residues,
methylation of the .alpha.-amino groups of lysine, arginine, and
histidine side chains [T. E. Creighton, Proteins: Structure and
Molecular Properties, W. H. Freeman & Co., San Francisco, pp.
79-86 (1983)], acetylation of the N-terminal amine, and amidation
of any C-terminal carboxyl group.
[0080] Another type of covalent modification of a polypeptide
included within the scope of this invention comprises altering the
native glycosylation pattern of the polypeptide. "Altering the
native glycosylation pattern" is intended for purposes herein to
mean deleting one or more carbohydrate moieties found in native
sequence polypeptide, and/or adding one or more glycosylation sites
that are not present in the native sequence polypeptide.
[0081] Addition of glycosylation sites to polypeptides may be
accomplished by altering the amino acid sequence thereof. The
alteration may be made, for example, by the addition of, or
substitution by, one or more serine or threonine residues to the
native sequence polypeptide (for O-linked glycosylation sites). The
amino acid sequence may optionally be altered through changes at
the DNA level, particularly by mutating the DNA encoding the
polypeptide at preselected bases such that codons are generated
that will translate into the desired amino acids.
[0082] Another means of increasing the number of carbohydrate
moieties on a polypeptide is by chemical or enzymatic coupling of
glycosides to the polypeptide. Such methods are described in the
art, e.g., in WO 87/05330 published 11 Sep. 1987, and in Aplin and
Wriston, CRC Crit. Rev. Biochem., pp. 259-306 (1981).
[0083] Removal of carbohydrate moieties present on the polypeptide
may be accomplished chemically or enzymatically or by mutational
substitution of codons encoding for amino acid residues that serve
as targets for glycosylation. Chemical deglycosylation techniques
are known in the art and described, for instance, by Hakimuddin, et
al., Arch. Biochem. Biophys., 259:52 (1987) and by Edge et al.,
Anal. Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate
moieties on polypeptides can be achieved by the use of a variety of
endo- and exo-glycosidases as described by Thotakura et al., Meth.
Enzymol., 138:350 (1987).
[0084] Another type of covalent modification of a protein comprises
linking the polypeptide to one of a variety of nonproteinaceous
polymers, e.g., polyethylene glycol, polypropylene glycol, or
polyoxyalkylenes, in the manner set forth in U.S. Pat. No.
4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or
4,179,337.
[0085] Polypeptides of the present invention may also be modified
in a way to form chimeric molecules comprising a first polypeptide
fused to another, heterologous polypeptide or amino acid sequence.
In one embodiment, such a chimeric molecule comprises a fusion of a
ubiquitin polypeptide (or an E2 or an E3, as defined below) with a
tag polypeptide which provides an epitope to which an anti-tag
antibody can selectively bind. The epitope tag is generally placed
at the amino- or carboxyl-terminus of the polypeptide. The presence
of such epitope-tagged forms of a polypeptide can be detected using
an antibody against the tag polypeptide. Also, providing an epitope
tag enables the polypeptide to be readily purified by affinity
purification using an anti-tag antibody or another type of affinity
matrix that binds to the epitope tag. In an alternative embodiment,
the chimeric molecule may comprise a fusion of a polypeptide
disclosed herein with an immunoglobulin or a particular region of
an immunoglobulin. For a bivalent form of the chimeric molecule,
such a fusion could be to the Fc region of an IgG molecule. Tags
for components of the invention are defined and described in detail
below.
[0086] The present invention provides methods for assaying
ubiquitin ligase activity. By "ubiquitin ligase" is meant a
ubiquitination enzyme capable of catalyzing the covalent binding of
a ubiquitin to another protein. Preferred embodiments of the
invention involve combining ubiquitin and ubiquitination enzymes,
including ubiquitin ligase, under conditions in which
ubiquitination may take place, and measuring the amount of
ubiquitin (polyubiquitin) bound to the ubiquitin ligase. In a
preferred embodiment, the ubiquitin ligase is an E3 ubiquitin
ligase, defined below.
[0087] Embodiments of the present invention involve binding
ubiquitin to a ubiquitination substrate protein. By "ubiquitination
substrate protein" is meant a protein to which the ubiquitin ligase
can catalyze the covalent binding of ubiquitin and includes target
proteins and ubiquitin. In a preferred embodiment, the
ubiquitination substrate protein is ubiquitin and the ubiquitin
ligase catalyzes the formation of polyubiquitin chains. In a
preferred embodiment, the polyubiquitin chains are formed by the
ubiquitin ligase in the absence of any target protein.
[0088] In one aspect, the invention provides methods for assaying
ubiquitination. In these assays, the interaction of the different
ubiquitination enzymes, the interaction of different subunits of
individual ubiquitination enzymes, and the influence of candidate
ubiquitination modulators can be observed and measured.
[0089] In a preferred embodiment, the invention is directed to a
method of assaying ubiquitin ligase activity. By "ubiquitin ligase
activity", "ubiquitin ligation" and grammatical equivalents thereof
is meant the catalysis of the covalent binding of ubiquitin to a
substrate protein. Preferably, each ubiquitin is bound such that a
subsequent ubiquitin polypeptide may be bound to it, to form chains
comprising a plurality of ubiquitin molecules. In a preferred
embodiment, ubiquitin ligase activity occurs in the absence of
target proteins, thus the substrate protein is ubiquitin.
[0090] In a preferred embodiment, the invention is additionally
directed to a method of assaying ubiquitin activating activity. By
"ubiquitin activating activity", "ubiquitin activation" and
grammatical equivalents thereof is meant the binding of ubiquitin
and E1. Preferably, E1 forms a high energy thiolester bond with the
ubiquitin.
[0091] In a preferred embodiment, the invention is also directed to
a method of assaying ubiquitin conjugating activity. By "ubiquitin
conjugating activity", "ubiquitin conjugation" and grammatical
equivalents thereof is meant the binding of activated ubiquitin
with an E2. As will be appreciated by those in the art, due to the
presence of the high energy thiolester bond in the E2-ubiquitin
conjugate, conjugated ubiquitin may be joined to other ubiquitin at
a low rate in the absence of the catalytic activity of E3.
Therefore, some of the ubiquitin measured in a ubiquitin
conjugating activity assay will be in the form of
poly-ubiquitin.
[0092] The present invention provides methods and compositions
comprising combining ubiquitin with other components. By
"combining" is meant the addition of the various components into a
receptacle under conditions in which ubiquitin ligase activity or
ubiquitination may take place. In a preferred embodiment, the
receptacle is a well of a 96 well plate or other commercially
available multiwell plate. In an alternate preferred embodiment,
the receptacle is the reaction vessel of a FACS machine. Other
receptacles useful in the present invention include, but are not
limited to 384 well plates and 1536 well plates. Still other
receptacles useful in the present invention will be apparent to the
skilled artisan.
[0093] The addition of the components may be sequential or in a
predetermined order or grouping, as long as the conditions amenable
to ubiquitin ligase activity are obtained. Such conditions are well
known in the art, and further guidance is provided below.
[0094] In a preferred embodiment, one or more components of the
present invention comprise a tag. By "tag" is meant an attached
molecule or molecules useful for the identification or isolation of
the attached component. Components having a tag are referred to as
"tag-X", wherein X is the component. For example, a ubiquitin
comprising a tag is referred to herein as "tag-ubiquitin".
Preferably, the tag is covalently bound to the attached component.
When more than one component of a combination has a tag, the tags
will be numbered for identification, for example "tag1-lubiquitin".
Components may comprise more than one tag, in which case each tag
will be numbered, for example "tag1,2-ubiquitin". Preferred tags
include, but are not limited to, a label, a partner of a binding
pair, and a surface substrate binding molecule. As will be evident
to the skilled artisan, many molecules may find use as more than
one type of tag, depending upon how the tag is used.
[0095] By "label" is meant a molecule that can be directly (i.e., a
primary label) or indirectly (i.e., a secondary label) detected;
for example a label can be visualized and/or measured or otherwise
identified so that its presence or absence can be known. As will be
appreciated by those in the art, the manner in which this is done
will depend on the label. Preferred labels include, but are not
limited to, fluorescent labels, label enzymes and
radioisotopes.
[0096] By "fluorescent label" is meant any molecule that may be
detected via its inherent fluorescent properties. Suitable
fluorescent labels include, but are not limited to, fluorescein,
rhodamine, tetramethylrhodamine, eosin, erythrosin, coumarin,
methyl-coumarins, pyrene, Malacite green, stilbene, Lucifer Yellow,
Cascade Blue.TM., Texas Red, IAEDANS, EDANS, BODIPY FL, LC Red 640,
Cy 5, Cy 5.5, LC Red 705 and Oregon green. Suitable optical dyes
are described in the 1996 Molecular Probes Handbook by Richard P.
Haugland, hereby expressly incorporated by reference. Suitable
fluorescent labels also include, but are not limited to, green
fluorescent protein (GFP; Chalfie, et al., Science
263(5148):802-805 (Feb. 11, 1994); and EGFP; Clontech--Genbank
Accession Number U55762), blue fluorescent protein (BFP; 1. Quantum
Biotechnologies, Inc. 1801 de Maisonneuve Blvd. West, 8th Floor,
Montreal (Quebec) Canada H3H 1J9; 2. Stauber, R. H. Biotechniques
24(3):462-471 (1998); 3. Heim, R. and Tsien, R. Y. Curr. Biol.
6:178-182 (1996)), enhanced yellow fluorescent protein (EYFP; 1.
Clontech Laboratories, Inc., 1020 East Meadow Circle, Palo Alto,
Calif. 94303), luciferase (Ichiki, et al., J. Immunol.
150(12):5408-5417 (1993)), .beta.-galactosidase (Nolan, et al.,
Proc Natl Acad Sci USA 85(8):2603-2607 (April 1988)) and Renilla WO
92/15673; WO 95/07463; WO 98/14605; WO 98/26277; WO 99/49019; U.S.
Pat. No. 5,292,658; U.S. Pat. No. 5,418,155; U.S. Pat. No.
5,683,888; U.S. Pat. No. 5,741,668; U.S. Pat. No. 5,777,079; U.S.
Pat. No. 5,804,387; U.S. Pat. No. 5,874,304; U.S. Pat. No.
5,876,995; and U.S. Pat. No. 5,925,558) All of the above-cited
references are expressly incorporated herein by reference.
[0097] In some instances, multiple fluorescent labels are employed.
In a preferred embodiment, at least two fluorescent labels are used
which are members of a fluorescence resonance energy transfer
(FRET) pair. FRET is phenomenon known in the art wherein excitation
of one fluorescent dye is transferred to another without emission
of a photon. A FRET pair consists of a donor fluorophore and an
acceptor fluorophore. The fluorescence emission spectrum of the
donor and the fluorescence absorption spectrum of the acceptor must
overlap, and the two molecules must be in close proximity. The
distance between donor and acceptor at which 50% of donors are
deactivated (transfer energy to the acceptor) is defined by the
Forster radius (R.sub.o), which is typically 10-100 .ANG.. Changes
in the fluorescence emission spectrum comprising FRET pairs can be
detected, indicating changes in the number of that are in close
proximity (i.e., within 100 .ANG. of each other). This will
typically result from the binding or dissociation of two molecules,
one of which is labeled with a FRET donor and the other of which is
labeled with a FRET acceptor, wherein such binding brings the FRET
pair in close proximity. Binding of such molecules will result in
an increased fluorescence emission of the acceptor and/or quenching
of the fluorescence emission of the donor.
[0098] FRET pairs (donor/acceptor) useful in the invention include,
but are not limited to, EDANS/fluorescein, IAEDANS/fluorescein,
fluorescein/tetramethylrhodamine, fluorescein/LC Red 640,
fluorescein/Cy 5, fluorescein/Cy 5.5 and fluorescein/LC Red
705.
[0099] In another aspect of FRET, a fluorescent donor molecule and
a nonfluorescent acceptor molecule ("quencher") may be employed. In
this application, fluorescent emission of the donor will increase
when quencher is displaced from close proximity to the donor and
fluorescent emission will decrease when the quencher is brought
into close proximity to the donor. Useful quenchers include, but
are not limited to, DABCYL, QSY 7 and QSY 33. Useful fluorescent
donor/quencher pairs include, but are not limited to EDANS/DABCYL,
Texas Red/DABCYL, BODIPY/DABCYL, Lucifer yellow/DABCYL,
coumarin/DABCYL and fluorescein/QSY 7 dye.
[0100] The skilled artisan will appreciate that FRET and
fluorescence quenching allow for monitoring of binding of labeled
molecules over time, providing continuous information regarding the
time course of binding reactions.
[0101] It is important to remember that ubiquitin is ligated to
substrate protein by its terminal carboxyl group to a lysine
residue, including lysine residues on other ubiquitin. Therefore,
attachment of labels or other tags should not interfere with either
of these active groups on the ubiquitin. Amino acids may be added
to the sequence of protein, through means well known in the art and
described herein, for the express purpose of providing a point of
attachment for a label. In a preferred embodiment, one or more
amino acids are added to the sequence of a component for attaching
a tag thereto, preferably a fluorescent label. In a preferred
embodiment, the amino acid to which a fluorescent label is attached
is Cysteine.
[0102] By "label enzyme" is meant an enzyme which may be reacted in
the presence of a label enzyme substrate which produces a
detectable product. Suitable label enzymes for use in the present
invention include but are not limited to, horseradish peroxidase,
alkaline phosphatase and glucose oxidase. Methods for the use of
such substrates are well known in the art. The presence of the
label enzyme is generally revealed through the enzyme's catalysis
of a reaction with a label enzyme substrate, producing an
identifiable product. Such products may be opaque, such as the
reaction of horseradish peroxidase with tetramethyl benzedine, and
may have a variety of colors. Other label enzyme substrates, such
as Luminol (available from Pierce Chemical Co.), have been
developed that produce fluorescent reaction products. Methods for
identifying label enzymes with label enzyme substrates are well
known in the art and many commercial kits are available. Examples
and methods for the use of various label enzymes are described in
Savage et al., Previews 247:6-9 (1998), Young, J. Virol. Methods
24:227-236 (1989), which are each hereby incorporated by reference
in their entirety.
[0103] By "radioisotope" is meant any radioactive molecule.
Suitable radioisotopes for use in the invention include, but are
not limited to .sup.14C, .sup.3H, .sup.32P, .sup.33P, .sup.35S,
.sup.125I, and .sup.131I. The use of radioisotopes as labels is
well known in the art.
[0104] In addition, labels may be indirectly detected, that is, the
tag is a partner of a binding pair. By "partner of a binding pair"
is meant one of a first and a second moiety, wherein said first and
said second moiety have a specific binding affinity for each other.
Suitable binding pairs for use in the invention include, but are
not limited to, antigens/antibodies (for example,
digoxigenin/anti-digoxigenin, dinitrophenyl (DNP)/anti-DNP,
dansyl-X-anti-dansyl, Fluorescein/anti-fluorescein, lucifer
yellow/anti-lucifer yellow, and rhodamine/anti-rhodamine),
biotin/avidin (or biotin/streptavidin) and calmodulin binding
protein (CBP)/calmodulin. Other suitable binding pairs include
polypeptides such as the FLAG-peptide (DYKDDDDK; SEQ ID NO:16)
[Hopp et al., BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope
peptide [Martin et al., Science, 255:192-194 (1992)]; tubulin
epitope peptide [Skinner et al., J. Biol. Chem., 266:15163-15166
(1991)]; and the T7 gene 10 protein peptide tag [Lutz-Freyermuth et
al., Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)] and the
antibodies each thereto. Generally, in a preferred embodiment, the
smaller of the binding pair partners serves as the tag, as steric
considerations in ubiquitin ligation may be important. As will be
appreciated by those in the art, binding pair partners may be used
in applications other than for labeling, as is further described
below.
[0105] As will be appreciated by those in the art, a partner of one
binding pair may also be a partner of another binding pair. For
example, an antigen (first moiety) may bind to a first antibody
(second moiety) which may, in turn, be an antigen for a second
antibody (third moiety). It will be further appreciated that such a
circumstance allows indirect binding of a first moiety and a third
moiety via an intermediary second moiety that is a binding pair
partner to each.
[0106] As will be appreciated by those in the art, a partner of a
binding pair may comprise a label, as described above. It will
further be appreciated that this allows for a tag to be indirectly
labeled upon the binding of a binding partner comprising a label.
Attaching a label to a tag which is a partner of a binding pair, as
just described, is referred to herein as "indirect labeling".
[0107] By "surface substrate binding molecule" and grammatical
equivalents thereof is meant a molecule have binding affinity for a
specific surface substrate, which substrate is generally a member
of a binding pair applied, incorporated or otherwise attached to a
surface. Suitable surface substrate binding molecules and their
surface substrates include, but are not limited to poly-histidine
(poly-his) or poly-histidine-glycine (poly-his-gly) tags and Nickel
substrate; the Glutathione-S Transferase tag and its antibody
substrate (available from Pierce Chemical); the flu HA tag
polypeptide and its antibody 12CA5 substrate [Field et al., Mol.
Cell. Biol., 8:2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7,
6E10, G4, B7 and 9E10 antibody substrates thereto [Evan et al.,
Molecular and Cellular Biology, 5:3610-3616 (1985)]; and the Herpes
Simplex virus glycoprotein D (gD) tag and its antibody substrate
[Paborsky et al., Protein Engineering, 3(6):547-553 (1990)]. In
general, surface binding substrate molecules useful in the present
invention include, but are not limited to, polyhistidine structures
(His-tags) that bind nickel substrates, antigens that bind to
surface substrates comprising antibody, haptens that bind to avidin
substrate (e.g., biotin) and CBP that binds to surface substrate
comprising calmodulin.
[0108] Production of antibody-embedded substrates is well known;
see Slinkin et al., Bioconj. Chem. 2:342-348 (1991); Torchilin et
al., supra; Trubetskoy et al., Bioconj. Chem. 3:323-327 (1992);
King et al., Cancer Res. 54:6176-6185 (1994); and Wilbur et al.,
Bioconjugate Chem. 5:220-235 (1994) (all of which are hereby
expressly incorporated by reference), and attachment of or
production of proteins with antigens is described above.
[0109] Calmodulin-embedded substrates are commercially available,
and production of proteins with CBP is described in Simcox et al.,
Strategies 8:40-43 (1995), which is hereby incorporated by
reference in its entirety.
[0110] As will be appreciated by those in the art, tag-components
of the invention can be made in various ways, depending largely
upon the form of the tag. Components of the invention and tags are
preferably attached by a covalent bond.
[0111] The production of tag-polypeptides by recombinant means when
the tag is also a polypeptide is described below. Production of
FLAG (DYKDDDDK; SEQ ID NO: 16)-labeled proteins is well known in
the art and kits for such production are commercially available
(for example, from Kodak and Sigma). Methods for the production and
use of FLAG (DYKDDDDK; SEQ ID NO: 16)-labeled proteins are found,
for example, in Winston et al., Genes and Devel. 13:270-283 (1999),
incorporated herein in its entirety, as well as product handbooks
provided with the above-mentioned kits.
[0112] Biotinylation of target molecules and substrates is well
known, for example, a large number of biotinylation agents are
known, including amine-reactive and thiol-reactive agents, for the
biotinylation of proteins, nucleic acids, carbohydrates, carboxylic
acids; see chapter 4, Molecular Probes Catalog, Haugland, 6th Ed.
1996, hereby incorporated by reference. A biotinylated substrate
can be attached to a biotinylated component via avidin or
streptavidin. Similarly, a large number of haptenylation reagents
are also known (Id.).
[0113] Methods for labeling of proteins with radioisotopes are
known in the art. For example, such methods are found in Ohta et
al., Molec. Cell 3:535-541 (1999), which is hereby incorporated by
reference in its entirety.
[0114] Production of proteins having His-tags by recombinant means
is well known, and kits for producing such proteins are
commercially available. Such a kit and its use is described in the
QIAexpress Handbook from Quiagen by Joanne Crowe et al., hereby
expressly incorporated by reference.
[0115] The functionalization of labels with chemically reactive
groups such as thiols, amines, carboxyls, etc. is generally known
in the art. In a preferred embodiment, the tag is functionalized to
facilitate covalent attachment.
[0116] The covalent attachment of the tag may be either direct or
via a linker. In one embodiment, the linker is a relatively short
coupling moiety, that is used to attach the molecules. A coupling
moiety may be synthesized directly onto a component of the
invention, ubiquitin for example, and contains at least one
functional group to facilitate attachment of the tag.
Alternatively, the coupling moiety may have at least two functional
groups, which are used to attach a functionalized component to a
functionalized tag, for example. In an additional embodiment, the
linker is a polymer. In this embodiment, covalent attachment is
accomplished either directly, or through the use of coupling
moieties from the component or tag to the polymer. In a preferred
embodiment, the covalent attachment is direct, that is, no linker
is used. In this embodiment, the component preferably contains a
functional group such as a carboxylic acid which is used for direct
attachment to the functionalized tag. It should be understood that
the component and tag may be attached in a variety of ways,
including those listed above. What is important is that manner of
attachment does not significantly alter the functionality of the
component. For example, in tag-ubiquitin, the tag should be
attached in such a manner as to allow the ubiquitin to be
covalently bound to other ubiquitin to form polyubiquitin chains.
As will be appreciated by those in the art, the above description
of covalent attachment of a label and ubiquitin applies equally to
the attachment of virtually any two molecules of the present
disclosure.
[0117] In a preferred embodiment, the tag is functionalized to
facilitate covalent attachment, as is generally outlined above.
Thus, a wide variety of tags are commercially available which
contain functional groups, including, but not limited to,
isothiocyanate groups, amino groups, haloacetyl groups, maleimides,
succinimidyl esters, and sulfonyl halides, all of which may be used
to covalently attach the tag to a second molecule, as is described
herein. The choice of the functional group of the tag will depend
on the site of attachment to either a linker, as outlined above or
a component of the invention. Thus, for example, for direct linkage
to a carboxylic acid group of a ubiquitin, amino modified or
hydrazine modified tags will be used for coupling via carbodiimide
chemistry, for example using
1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDAC) as is known
in the art (see Set 9 and Set 11 of the Molecular Probes Catalog,
supra; see also the Pierce 1994 Catalog and Handbook, pages T-155
to T-200, both of which are hereby incorporated by reference). In
one embodiment, the carbodiimide is first attached to the tag, such
as is commercially available for many of the tags described
herein.
[0118] In a preferred embodiment, ubiquitin is in the form of
tag-ubiquitin.
[0119] In a preferred embodiment, ubiquitin is in the form of
tag-ubiquitin, wherein, tag is a partner of a binding pair.
Preferably in this embodiment the tag is FLAG (DYKDDDDK; SEQ ID NO:
16) and the binding partner is anti-FLAG (DYKDDDDK; SEQ ID NO: 16).
Preferably in this embodiment, a label is attached to the FLAG
(DYKDDDDK; SEQ ID NO: 16) by indirect labeling. Preferably, the
label is a label enzyme. Most preferably, the label enzyme is
horseradish peroxidase, which is reacted with a fluorescent label
enzyme substrate. Preferably, the label enzyme substrate is
Luminol. Alternatively, the label is a fluorescent label.
[0120] In another preferred embodiment, ubiquitin is in the form of
tag-ubiquitin, wherein the tag is a fluorescent label. In a
particularly preferred embodiment, ubiquitin is in the form of
tag1-ubiquitin and tag2-ubiquitin, wherein tag1 and tag2 are the
members of a FRET pair. In an alternate preferred embodiment,
ubiquitin is in the form of tag1-ubiquitin and tag2-ubiquitin,
wherein tag1 is a fluorescent label and tag2 is a quencher of the
fluorescent label. In either of these preferred embodiments, when
tag1-ubiquitin and tag2-ubiquitin are bound through the activity of
a ubiquitin ligase, preferably tag1 and tag2 are within 100 .ANG.
of each other, more preferable within 70 .ANG., still more
preferably within 50 .ANG., even more preferably within 40 .ANG.,
and in some cases, preferably within 30 .ANG. or less.
[0121] In yet another preferred embodiment, ubiquitin is in the
form of tag1,2-ubiquitin and tag1,3-ubiquitin, wherein tag1 is a
member of a binding pair, preferably FLAG (DYKDDDDK; SEQ ID NO:
16), tag2 is a fluorescent label and tag3 is either a fluorescent
label such that tag2 and tag3 are members of a FRET pair or tag3 is
a quencher of tag2.
[0122] In a preferred embodiment, one or more amino acids are added
to the ubiquitin sequence, using recombinant techniques as
described herein, to provide an attachment point for a tag,
preferably a fluorescent label or a quencher. In a preferred
embodiment, the one or more amino acids are Cys or Ala-Cys.
Preferably, the one or more amino acids are attached to the
N-terminal of the ubiquitin. In a preferred embodiment, the one or
more amino acids intervenes the sequence of a FLAG (DYKDDDDK; SEQ
ID NO: 16) tag and the ubiquitin. In a preferred embodiment, the
tag, preferably a fluorescent label or a quencher, is attached to
the added Cysteine.
[0123] The present invention provides methods and compositions
comprising combining ubiquitin and E1. By "E1" is meant a ubiquitin
activating enzyme. In a preferred embodiment, E1 is capable of
transferring ubiquitin to an E2, defined below. In a preferred
embodiment, E1 binds ubiquitin. In a preferred embodiment, E1 forms
a high energy thiolester bond with ubiquitin, thereby "activating"
the ubiquitin.
[0124] In a preferred embodiment, E1 proteins useful in the
invention include those having the amino acid sequence of the
polypeptide having ATCC accession numbers A38564, S23770, AAA61246,
P22314, CAA40296 and BAA33144, incorporated herein by reference. In
a preferred embodiment, E1 has the amino acid sequence shown in
FIG. 6B or is encoded by a nucleic acid comprising the sequence
shown in FIG. 6A. Preferably E1 is human E1. E1 is commercially
available from Affiniti Research Products (Exeter, U.K.).
[0125] In a preferred embodiment, nucleic acids which may be used
for producing E1 proteins for the invention include, but are not
limited to, those disclosed by ATCC accession numbers M58028,
X56976 and AB012190, incorporated herein by reference. In a
preferred embodiment, E1 is encoded by a nucleic acid having a
sequence consisting essentially of the sequence shown in FIG. 6A.
Variants of the cited E1 proteins, also included in the term "E1",
can be made as described herein.
[0126] In a preferred embodiment, the compositions of the invention
comprise E2. By "E2" is meant a ubiquitin carrier enzyme (also
known as a ubiquitin conjugating enzyme). In a preferred
embodiment, ubiquitin is transferred from E1 to E2. In a preferred
embodiment, the transfer results in a thiolester bond formed
between E2 and ubiquitin. In a preferred embodiment, E2 is capable
of transferring ubiquitin to an E3, defined below. In a preferred
embodiment, the ubiquitination substrate protein is ubiquitin.
[0127] In a preferred embodiment, proteins which may be used in the
present invention as E2 include, but are not limited to, those
having the amino acid sequences disclosed in ATCC accession numbers
AAC37534, P49427, CAA82525, AAA58466, AAC41750, P51669, AAA91460,
AAA91461, CAA63538, AAC50633, P27924, AAB36017, Q16763, AAB86433,
AAC26141, CAA04156, BAA11675, Q16781, NP.sub.--003333, BAB18652,
AAH00468, CAC16955, CAB76865, CAB76864, NP.sub.--05536, O00762,
XP.sub.--009804, XP.sub.--009488, XP.sub.--006823, XP.sub.--006343,
XP.sub.--005934, XP.sub.--002869, XP.sub.--003400, XP.sub.--009365,
XP.sub.--010361, XP.sub.--004699, XP.sub.--004019, O14933, P27924,
P50550, P52485, P51668, P51669, P49459, P37286, P23567, P56554, and
CAB45853, each of which is incorporated herein by reference.
Particularly preferred are sequences disclosed in ATCC accession
numbers NP003331, NP003330, NP003329, P49427, AAB53362, NP008950,
XP009488 and AAC41750, also incorporated by reference. The skilled
artisan will appreciate that many different E2 proteins and
isozymes are known in the filed and may be used in the present
invention, provided that the E2 has ubiquitin conjugating activity.
Also specifically included within the term "E2" are variants of E2,
which can be made as described herein.
[0128] In a preferred embodiment, E2 is one of Ubc5 (Ubch5,
preferably Ubch5c), Ubc3 (Ubch3), Ubc4 (Ubch4) and UbcX (Ubc 10,
Ubch 10). In a preferred embodiment, E2 is Ubc5c. In a preferred
embodiment, E2 has the amino acid sequence shown in FIG. 7B or is
encoded by a nucleic acid consisting essentially of the sequence
shown in FIG. 7A.
[0129] In a preferred embodiment, nucleic acids which may be used
to make E2 include, but are not limited to, those nucleic acids
having sequences disclosed in ATCC accession numbers L2205, Z29328,
M92670, L40146, U39317, U39318, X92962, U58522, S81003, AF031141,
AF075599, AJ000519, XM009488, NM007019, U73379, L40146 and D83004,
each of which is incorporated herein by reference. As described
above, variants of these and other E2 encoding nucleic acids may
also be used to make variant E2 proteins.
[0130] In a preferred embodiment, the nucleic acid used to make E2
comprises the sequence shown in FIG. 7A.
[0131] In a preferred embodiment, E2 has a tag, as defined above,
with the complex being referred to herein as "tag-E2". Preferred E2
tags include, but are not limited to, labels, partners of binding
pairs and substrate binding elements. In a most preferred
embodiment, the tag is a His-tag or GST tag.
[0132] The present invention provides methods and compositions
comprising E3. By "E3" is meant a ubiquitin ligase, as defined
above, comprising one or more components associated with ligation
of ubiquitin to a ubiquitination substrate protein for
ubiquitin-dependent proteolysis. In a preferred embodiment, E3
comprises a ring finger protein and a Cullin. In a preferred
embodiment, RING finger proteins include, but are not limited to,
ROC1, ROC2 and APC11. In a preferred embodiment, Cullins include,
but are not limited to, CUL1, CUL2, CUL3, CUL4A, CUL4B, CUL5 and
APC2.
[0133] In a preferred embodiment, RING finger proteins include, but
are not limited to, proteins having the amino acid sequence
disclosed in ATCC accession numbers AAD30147 and AAD30146 and
6320196, incorporated herein by reference. In a more preferred
embodiment, the ring finger protein has a sequence selected from
the group consisting of that shown in FIG. 8, FIG. 9 and FIG.
10B.
[0134] In a preferred embodiment, Cullins include, but are not
limited to, proteins having the amino acid sequences disclosed in
ATCC accession numbers 4503161, AAC50544, AAC36681, 4503163,
AAC51190, AAD23581, 4503165, AAC36304, AAC36682, AAD45191,
AAC50548, Q13620, 4503167 and AAF05751, each of which is
incorporated herein by reference. In addition, in the context of
the invention, each of the RING finger proteins and Cullins
encompass variants of the known or listed sequences, as described
herein.
[0135] In a preferred embodiment, the Cullin has a sequence as
shown in FIG. 11B or 12B.
[0136] These E3 proteins and variants may be made as described
herein. In a preferred embodiment, nucleic acids used to make the
RING finger proteins include, but are not limited to, those having
the nucleic acid sequences disclosed in ATCC accession numbers
AF142059, AF142060 and nucleic acids 433493 to 433990 of NC 001136.
In a preferred embodiment, Cullins are made from nucleic acids
including, but not limited to, those having nucleic acid sequences
disclosed in ATCC accession numbers NM 003592, U58087, AF062536,
AF126404, NM 003591, U83410, NM 003590, AB014517, AF062537,
AF064087, AF077188, U58091, NM 003478, X81882 and AF191337, each of
which is incorporated herein by reference. As described above,
variants of these sequences are also encompassed by the
invention.
[0137] In a preferred embodiment, nucleic acid used to produce ROC2
comprises the sequence depicted in FIG. 12A. In a preferred
embodiment, nucleic acid used to produce CUL5 comprises the
sequence depicted in FIG. 13A. In a preferred embodiment, nucleic
acid used to produce APC2 comprises the sequence depicted in FIG.
14A.
[0138] In a preferred embodiment, E3 comprises the RING finger
protein/Cullin combination APC11/APC2. In another preferred
embodiment, E3 comprises the RING finger protein/Cullin combination
ROC1/CUL1. In yet preferred embodiment, E3 comprises the RING
finger protein/Cullin combination ROC1/CUL2. Instill another
preferred embodiment, E3 comprises the RING finger protein/Cullin
combination ROC2/CUL5. However, the skilled artisan will appreciate
that any combination of E3 components may be produced and used in
the invention described herein.
[0139] In an alternate embodiment, E3 comprises the ligase
E3-alpha, E3A (E6-AP), HERC2, SMURF1, TRAF6, MDM2, Cbl, Sina/Siah,
Itchy, IAP or NEDD-4. In this embodiment, the ligase has the amino
acid sequence of that disclosed in ATCC accession number AAC39845,
Q05086, CAA66655, CAA66654, CAA66656, AAD08657, NP.sub.--002383,
XP.sub.--006284, AAC51970, XP.sub.--013050, BAB39389, Q00987,
AAF08298 or P46934, each of which is incorporated herein by
reference. As above, variants are also encompassed by the
invention. Nucleic acids for making E3 for this embodiment include,
but are not limited to, those having the sequences disclosed in
ATCC accession numbers AF061556, XM006284, U76247, XM013050,
X898032, X98031, X98033, AF071172, Z12020, AB056663, AF199364 and
D42055 and variants thereof.
[0140] E3 may also comprise other components, such as SKP1 and
F-box proteins. The amino acid and nucleic acid sequences for SKP1
are found in ATCC accession numbers AAC50241 and U33760,
respectively. Many F-box proteins are known in the art and their
amino acid and nucleic acid sequences are readily obtained by the
skilled artisan from various published sources.
[0141] In a preferred embodiment, the E3 components are produced
recombinantly, as described herein.
[0142] In a preferred embodiment, the E3 components are
co-expressed in the same host cell. Co-expression may be achieved
by transforming the cell with a vector comprising nucleic acids
encoding two or more of the E3 components, or by transforming the
host cell with separate vectors, each comprising a single component
of the desired E3 protein complex. In a preferred embodiment, the
RING finger protein and Cullin are expressed in a single host
transfected with two vectors, each comprising nucleic acid encoding
one or the other polypeptide, as described in further detail in the
Examples.
[0143] In a preferred embodiment, E3 has a tag, which complex is
referred to herein as "tag-E3". Preferably, the tag is attached to
only one component of the E3. Preferred E3 tags include, but are
not limited to, labels, partners of binding pairs and substrate
binding elements. More preferably, the tag is a surface substrate
binding molecule. Most preferably, the tag is a His-tag or GST
tag.
[0144] In an embodiment herein, ubiquitin and ubiquitination
enzymes and their components are cloned and expressed as outlined
below. Thus, probe or degenerate polymerase chain reaction (PCR)
primer sequences may be used to find other related ubiquitination
proteins from humans or other organisms. As will be appreciated by
those in the art, particularly useful probe and/or PCR primer
sequences include the unique areas of a nucleic acid sequence. As
is generally known in the art, preferred PCR primers are from about
15 to about 35 nucleotides in length, with from about 20 to about
30 being preferred, and may contain inosine as needed. The
conditions for the PCR reaction are well known in the art. It is
therefore also understood that provided along with the sequences in
the sequences cited herein are portions of those sequences, wherein
unique portions of 15 nucleotides or more are particularly
preferred. The skilled artisan can routinely synthesize or cut a
nucleotide sequence to the desired length.
[0145] Once isolated from its natural source, e.g., contained
within a plasmid or other vector or excised therefrom as a linear
nucleic acid segment, the recombinant nucleic acid can be further
used as a probe to identify and isolate other nucleic acids. It can
also be used as a "precursor" nucleic acid to make modified or
variant nucleic acids and proteins.
[0146] Using the nucleic acids of the present invention which
encode a protein, a variety of expression vectors are made. The
expression vectors may be either self-replicating extrachromosomal
vectors or vectors which integrate into a host genome. Generally,
these expression vectors include transcriptional and translational
regulatory nucleic acid operably linked to the nucleic acid
encoding the protein. The term "control sequences" refers to DNA
sequences necessary for the expression of an operably linked coding
sequence in a particular host organism. The control sequences that
are suitable for prokaryotes, for example, include a promoter,
optionally an operator sequence, and a ribosome binding site.
Eukaryotic cells are known to utilize promoters, polyadenylation
signals, and enhancers.
[0147] Nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide if it is expressed as a preprotein
that participates in the secretion of the polypeptide; a promoter
or enhancer is operably linked to a coding sequence if it affects
the transcription of the sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to
facilitate translation. As another example, operably linked refers
to DNA sequences linked so as to be contiguous, and, in the case of
a secretory leader, contiguous and in reading frame. However,
enhancers do not have to be contiguous. Linking is accomplished by
ligation at convenient restriction sites. If such sites do not
exist, the synthetic oligonucleotide adaptors or linkers are used
in accordance with conventional practice. The transcriptional and
translational regulatory nucleic acid will generally be appropriate
to the host cell used to express the protein; for example,
transcriptional and translational regulatory nucleic acid sequences
from Bacillus are preferably used to express the protein in
Bacillus. Numerous types of appropriate expression vectors, and
suitable regulatory sequences are known in the art for a variety of
host cells.
[0148] In general, the transcriptional and translational regulatory
sequences may include, but are not limited to, promoter sequences,
ribosomal binding sites, transcriptional start and stop sequences,
translational start and stop sequences, and enhancer or activator
sequences. In a preferred embodiment, the regulatory sequences
include a promoter and transcriptional start and stop
sequences.
[0149] Promoter sequences encode either constitutive or inducible
promoters. The promoters may be either naturally occurring
promoters or hybrid promoters. Hybrid promoters, which combine
elements of more than one promoter, are also known in the art, and
are useful in the present invention.
[0150] In addition, the expression vector may comprise additional
elements. For example, the expression vector may have two
replication systems, thus allowing it to be maintained in two
organisms, for example in mammalian or insect cells for expression
and in a procaryotic host for cloning and amplification.
Furthermore, for integrating expression vectors, the expression
vector contains at least one sequence homologous to the host cell
genome, and preferably two homologous sequences which flank the
expression construct. The integrating vector may be directed to a
specific locus in the host cell by selecting the appropriate
homologous sequence for inclusion in the vector. Constructs for
integrating vectors are well known in the art.
[0151] In addition, in a preferred embodiment, the expression
vector contains a selectable marker gene to allow the selection of
transformed host cells. Selection genes are well known in the art
and will vary with the host cell used.
[0152] A preferred expression vector system is a retroviral vector
system such as is generally described in PCT/US97/01019 and
PCT/US97/01048, both of which are hereby expressly incorporated by
reference.
[0153] Proteins of the present invention are produced by culturing
a host cell transformed with an expression vector containing
nucleic acid encoding the protein, under the appropriate conditions
to induce or cause expression of the protein. The conditions
appropriate for protein expression will vary with the choice of the
expression vector and the host cell, and will be easily ascertained
by one skilled in the art through routine experimentation. For
example, the use of constitutive promoters in the expression vector
will require optimizing the growth and proliferation of the host
cell, while the use of an inducible promoter requires the
appropriate growth conditions for induction. In addition, in some
embodiments, the timing of the harvest is important. For example,
the baculoviral systems used in insect cell expression are lytic
viruses, and thus harvest time selection can be crucial for product
yield.
[0154] Appropriate host cells include yeast, bacteria,
archaebacteria, fungi, and insect and animal cells, including
mammalian cells. Of particular interest are Drosophila melanogaster
cells, Pichia pastoris and P. methanolica, Saccharomyces cerevisiae
and other yeasts, E. Coli, Bacillus subtilis, SF9 cells, SF21
cells, C129 cells, Saos-2 cells, Hi-5 cells, 293 cells, Neurospora,
BHK, CHO, COS, and HeLa cells. Of greatest interest are Pichia
pastoris and P. methanolica, E. Coli, SF9 cells, SF21 cells and
Hi-5 cells.
[0155] In a preferred embodiment, the proteins are expressed in
mammalian cells. Mammalian expression systems are also known in the
art, and include retroviral systems. A mammalian promoter is any
DNA sequence capable of binding mammalian RNA polymerase and
initiating the downstream (3') transcription of a coding sequence
for a protein into mRNA. A promoter will have a transcription
initiating region, which is usually placed proximal to the 5' end
of the coding sequence, and a TATA box, using a located 25-30 base
pairs upstream of the transcription initiation site. The TATA box
is thought to direct RNA polymerase II to begin RNA synthesis at
the correct site. A mammalian promoter will also contain an
upstream promoter element (enhancer element), typically located
within 100 to 200 base pairs upstream of the TATA box. An upstream
promoter element determines the rate at which transcription is
initiated and can act in either orientation. Of particular use as
mammalian promoters are the promoters from mammalian viral genes,
since the viral genes are often highly expressed and have a broad
host range. Examples include the SV40 early promoter, mouse mammary
tumor virus LTR promoter, adenovirus major late promoter, herpes
simplex virus promoter, and the CMV promoter.
[0156] Typically, transcription termination and polyadenylation
sequences recognized by mammalian cells are regulatory regions
located 3' to the translation stop codon and thus, together with
the promoter elements, flank the coding sequence. The 3' terminus
of the mature mRNA is formed by site-specific post-translational
cleavage and polyadenylation. Examples of transcription terminator
and polyadenylation signals include those derived form SV40.
[0157] The methods of introducing exogenous nucleic acid into
mammalian hosts, as well as other hosts, is well known in the art,
and will vary with the host cell used. Techniques include
dextran-mediated transfection, calcium phosphate precipitation,
polybrene mediated transfection, protoplast fusion,
electroporation, viral infection, encapsulation of the
polynucleotide(s) in liposomes, and direct microinjection of the
DNA into nuclei.
[0158] In a preferred embodiment, proteins are expressed in
bacterial systems. Bacterial expression systems are well known in
the art.
[0159] A suitable bacterial promoter is any nucleic acid sequence
capable of binding bacterial RNA polymerase and initiating the
downstream (3') transcription of the coding sequence of a protein
into mRNA. A bacterial promoter has a transcription initiation
region which is usually placed proximal to the 5' end of the coding
sequence. This transcription initiation region typically includes
an RNA polymerase binding site and a transcription initiation site.
Sequences encoding metabolic pathway enzymes provide particularly
useful promoter sequences. Examples include promoter sequences
derived from sugar metabolizing enzymes, such as galactose, lactose
and maltose, and sequences derived from biosynthetic enzymes such
as tryptophan.
[0160] Promoters from bacteriophage may also be used and are known
in the art. In addition, synthetic promoters and hybrid promoters
are also useful; for example, the tac promoter is a hybrid of the
trp and tac promoter sequences. Furthermore, a bacterial promoter
can include naturally occurring promoters of non-bacterial origin
that have the ability to bind bacterial RNA polymerase and initiate
transcription.
[0161] In addition to a functioning promoter sequence, an efficient
ribosome binding site is desirable. In E. Coli, the ribosome
binding site is called the Shine-Delgarno (SD) sequence and
includes an initiation codon and a sequence 3-9 nucleotides in
length located 3-11 nucleotides upstream of the initiation
codon.
[0162] The expression vector may also include a signal peptide
sequence that provides for secretion of the protein in bacteria.
The signal sequence typically encodes a signal peptide comprised of
hydrophobic amino acids which direct the secretion of the protein
from the cell, as is well known in the art. The protein is either
secreted into the growth media (gram-positive bacteria) or into the
periplasmic space, located between the inner and outer membrane of
the cell (gram-negative bacteria).
[0163] The bacterial expression vector may also include a
selectable marker gene to allow for the selection of bacterial
strains that have been transformed. Suitable selection genes
include genes which render the bacteria resistant to drugs such as
ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and
tetracycline. Selectable markers also include biosynthetic genes,
such as those in the histidine, tryptophan and leucine biosynthetic
pathways.
[0164] These components are assembled into expression vectors.
Expression vectors for bacteria are well known in the art, and
include vectors for Bacillus subtilis, E. Coli, Streptococcus
cremoris, and Streptococcus lividans, among others.
[0165] The bacterial expression vectors are transformed into
bacterial host cells using techniques well known in the art, such
as calcium chloride treatment, electroporation, and others.
[0166] In one embodiment, proteins are produced in insect cells.
Expression vectors for the transformation of insect cells, and in
particular, baculovirus-based expression vectors, are well known in
the art.
[0167] In a preferred embodiment, proteins are produced in yeast
cells. Yeast expression systems are well known in the art, and
include expression vectors for Saccharomyces cerevisiae, Candida
albicans and C. maltosa, Hansenula polymorpha, Kluyveromyces
fragilis and K lactis, Pichia guillerimondii P. methanolica and P.
pastoris, Schizosaccharomyces pombe, and Yarrowia lipolytica.
Preferred promoter sequences for expression in yeast include the
inducible GAL1,10 promoter, the promoters from alcohol
dehydrogenase, enolase, glucokinase, glucose-6-phosphate isomerase,
glyceraldehyde 3-phosphate-dehydrogenase, hexokinase,
phosphofructokinase, 3-phosphoglycerate mutase, pyruvate kinase,
and the acid phosphatase gene. Yeast selectable markers include
ADE2, HIS4, LEU2, TRP1, and ALG7, which confers resistance to
tunicamycin; the neomycin phosphotransferase gene, which confers
resistance to G418; and the CUP1 gene, which allows yeast to grow
in the presence of copper ions.
[0168] The protein may also be made as a fusion protein, using
techniques well known in the art. Thus, for example, the protein
may be made as a fusion protein to increase expression, or for
other reasons. For example, when the protein is a peptide, the
nucleic acid encoding the peptide may be linked to other nucleic
acid for expression purposes. Similarly, proteins of the invention
can be linked to protein labels, such as green fluorescent protein
(GFP), red fluorescent protein (RFP), blue fluorescent protein
(BFP), yellow fluorescent protein (YFP), etc.
[0169] In a preferred embodiment, the protein is purified or
isolated after expression. Proteins may be isolated or purified in
a variety of ways known to those skilled in the art depending on
what other components are present in the sample. Standard
purification methods include electrophoretic, molecular,
immunological and chromatographic techniques, including ion
exchange, hydrophobic, affinity, and reverse-phase HPLC
chromatography, and chromatofocusing. For example, the ubiquitin
protein may be purified using a standard anti-ubiquitin antibody
column. Ultrafiltration and diafiltration techniques, in
conjunction with protein concentration, are also useful. For
general guidance in suitable purification techniques, see Scopes,
R., Protein Purification, Springer Verlag, NY (1982). The degree of
purification necessary will vary depending on the use of the
protein. In some instances no purification will be necessary.
[0170] Once made, the compositions find use in a number of
applications, including, but not limited to, screens for modulators
of ubiquitination. By "modulator" is meant a compound which can
increase or decrease ubiquitination. The skilled artisan will
appreciate that modulators of ubiquitination may affect enzyme
activity, enzyme interaction with the substrate, interaction
between ubiquitin and the substrate, or a combination of these. A
modulator that specifically affects ubiquitin ligase activity is a
ubiquitin ligase modulator.
[0171] By "candidate", "candidate agent", "candidate modulator",
"candidate ubiquitination modulator" or grammatical equivalents
herein is meant any molecule, e.g., proteins (which herein includes
proteins, polypeptides, and peptides), small organic or inorganic
molecules, polysaccharides, polynucleotides, etc. which are to be
tested for ubiquitination modulator activity. Candidate agents
encompass numerous chemical classes. In a preferred embodiment, the
candidate agents are organic molecules, particularly small organic
molecules, comprising functional groups necessary for structural
interaction with proteins, particularly hydrogen bonding, and
typically include at least an amine, carbonyl, hydroxyl or carboxyl
group, preferably at least two of the functional chemical groups.
The candidate agents often comprise cyclical carbon or heterocyclic
structures and/or aromatic or polyaromatic structures substituted
with one or more chemical functional groups.
[0172] Candidate modulators are obtained from a wide variety of
sources, as will be appreciated by those in the art, including
libraries of synthetic or natural compounds. As will be appreciated
by those in the art, the present invention provides a rapid and
easy method for screening any library of candidate modulators,
including the wide variety of known combinatorial chemistry-type
libraries.
[0173] In a preferred embodiment, candidate modulators are
synthetic compounds. Any number of techniques are available for the
random and directed synthesis of a wide variety of organic
compounds and biomolecules, including expression of randomized
oligonucleotides. See for example WO 94/24314, hereby expressly
incorporated by reference, which discusses methods for generating
new compounds, including random chemistry methods as well as
enzymatic methods. As described in WO 94/24314, one of the
advantages of the present method is that it is not necessary to
characterize the candidate modulator prior to the assay; only
candidate modulators that increase or decease ubiquitin ligase
activity need be identified. In addition, as is known in the art,
coding tags using split synthesis reactions may be done, to
essentially identify the chemical moieties tested.
[0174] Alternatively, a preferred embodiment utilizes libraries of
natural compounds in the form of bacterial, fungal, plant and
animal extracts that are available or readily produced.
[0175] Additionally, natural or synthetically produced libraries
and compounds are readily modified through conventional chemical,
physical and biochemical means. Known pharmacological agents may be
subjected to directed or random chemical modifications, including
enzymatic modifications, to produce structural analogs.
[0176] In a preferred embodiment, candidate modulators include
proteins, nucleic acids, and chemical moieties.
[0177] In a preferred embodiment, the candidate modulator are
proteins, as defined above. In a preferred embodiment, the
candidate modulators are naturally occurring proteins or fragments
of naturally occurring proteins. Thus, for example, cellular
extracts containing proteins, or random or directed digests of
proteinaceous cellular extracts, may be tested, as is more fully
described below. In this way libraries of procaryotic and
eucaryotic proteins may be made for screening against any number of
ubiquitin ligase compositions. Particularly preferred in this
embodiment are libraries of bacterial, fungal, viral, and mammalian
proteins, with the latter being preferred, and human proteins being
especially preferred.
[0178] In a preferred embodiment, the candidate modulators are
peptides of from about 2 to about 50 amino acids, with from about 5
to about 30 amino acids being preferred, and from about 8 to about
20 being particularly preferred. The peptides may be digests of
naturally occurring proteins as is outlined above, random peptides,
or "biased" random peptides. By "randomized" or grammatical
equivalents herein is meant that each nucleic acid and peptide
consists of essentially random nucleotides and amino acids,
respectively. Since generally these random peptides (or nucleic
acids, discussed below) are chemically synthesized, they may
incorporate any nucleotide or amino acid at any position. The
synthetic process can be designed to generate randomized proteins
or nucleic acids, to allow the formation of all or most of the
possible combinations over the length of the sequence, thus forming
a library of randomized candidate bioactive proteinaceous
agents.
[0179] The library should provide a sufficiently structurally
diverse population of randomized agents to effect a
probabilistically sufficient range of diversity to allow
interaction with a particular ubiquitin ligase enzyme. Accordingly,
an interaction library must be large enough so that at least one of
its members will have a structure that interacts with a ubiquitin
ligase enzyme. Although it is difficult to gauge the required
absolute size of an interaction library, nature provides a hint
with the immune response: a diversity of 10.sup.7-10.sup.8
different antibodies provides at least one combination with
sufficient affinity to interact with most potential antigens faced
by an organism. Published in vitro selection techniques have also
shown that a library size of 10.sup.7-10.sup.8 is sufficient to
find structures with affinity for a target. A library of all
combinations of a peptide 7 to 20 amino acids in length, such as
generally proposed herein, has the potential to code for 20.sup.7
(10.sup.9) to 20.sup.20. Thus, with libraries of 10.sup.7 to
10.sup.8 different molecules the present methods allow a "working"
subset of a theoretically complete interaction library for 7 amino
acids, and a subset of shapes for the 20.sup.20 library. Thus, in a
preferred embodiment, at least 10.sup.6, preferably at least
10.sup.7, more preferably at least 10.sup.8 and most preferably at
least 10.sup.9 different sequences are simultaneously analyzed in
the subject methods. Preferred methods maximize library size and
diversity.
[0180] In one embodiment, the library is fully randomized, with no
sequence preferences or constants at any position. In a preferred
embodiment, the library is biased. That is, some positions within
the sequence are either held constant, or are selected from a
limited number of possibilities. For example, in a preferred
embodiment, the nucleotides or amino acid residues are randomized
within a defined class, for example, of hydrophobic amino acids,
hydrophilic residues, sterically biased (either small or large)
residues, towards the creation of cysteines, for cross linking,
prolines for SH-3 domains, serines, threonines, tyrosines or
histidines for phosphorylation sites, etc., or to purines, etc.
[0181] In a preferred embodiment, the bias is towards peptides or
nucleic acids that interact with known classes of molecules. For
example, when the candidate modulator is a peptide, it is known
that much of intracellular signaling is carried out via short
regions of polypeptides interacting with other polypeptides through
small peptide domains. For instance, a short region from the HIV-1
envelope cytoplasmic domain has been previously shown to block the
action of cellular calmodulin. Regions of the Fas cytoplasmic
domain, which shows homology to the mastoparan toxin from Wasps,
can be limited to a short peptide region with death-inducing
apoptotic or G protein inducing functions. Magainin, a natural
peptide derived from Xenopus, can have potent anti-tumor and
anti-microbial activity. Short peptide fragments of a protein
kinase C isozyme (.beta.PKC), have been shown to block nuclear
translocation of .beta.PKC in Xenopus oocytes following
stimulation. And, short SH-3 target peptides have been used as
psuedosubstrates for specific binding to SH-3 proteins. This is of
course a short list of available peptides with biological activity,
as the literature is dense in this area. Thus, there is much
precedent for the potential of small peptides to have activity on
intracellular signaling cascades. In addition, agonists and
antagonists of any number of molecules may be used as the basis of
biased randomization of candidate modulators as well.
[0182] Thus, a number of molecules or protein domains are suitable
as starting points for the generation of biased randomized
candidate modulators. A large number of small molecule domains are
known, that confer a common function, structure or affinity. In
addition, as is appreciated in the art, areas of weak amino acid
homology may have strong structural homology. A number of these
molecules, domains, and/or corresponding consensus sequences, are
known, including, but are not limited to, SH-2 domains, SH-3
domains, Pleckstrin, death domains, protease cleavage/recognition
sites, enzyme inhibitors, enzyme substrates, Traf, etc.
[0183] In a preferred embodiment, the candidate modulators are
nucleic acids. With reference to candidate modulators, by "nucleic
acid" or "oligonucleotide" or grammatical equivalents herein means
at least two nucleotides covalently linked together. A nucleic acid
of the present invention will generally contain phosphodiester
bonds, although in some cases, as outlined below, nucleic acid
analogs are included that may have alternate backbones, comprising,
for example, phosphoramide (Beaucage et al., Tetrahedron
49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem.
35:3800 (1970); Sprinzl et al., Eur. J. Biochem. 81:579 (1977);
Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al.,
Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc.
110:4470 (1988); and Pauwels et al., Chemica Scripta 26:141
91986)), phosphorothioate (Mag et al., Nucleic Acids Res. 19:1437
(1991); and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et
al., J. Am. Chem. Soc. 111:2321 (1989), O-methylphophoroamidite
linkages (see Eckstein, Oligonucleotides and Analogues: A Practical
Approach, Oxford University Press), and peptide nucleic acid
backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895
(1992); Meier et al., Chem. Int. Ed. End. 31:1008 (1992); Nielsen,
Nature, 365:566 (1993); Carlsson et al., Nature 380:207 (1996), all
of which are incorporated by reference). Other analog nucleic acids
include those with positive backbones (Denpcy et al., Proc. Natl.
Acad. Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos.
5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863;
Kiedrowshi et al., Angew. Chem. Intl. Ed. English 30:423 (1991);
Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); Letsinger et
al., Nucleoside & Nucleotide 13:1597 (1994); Chapters 2 and 3,
ASC Symposium Series 580, "Carbohydrate Modifications in Antisense
Research", Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al.,
Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffs et al.,
J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743 (1996))
and nonribose backbones, including those described in U.S. Pat.
Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium
Series 580, "Carbohydrate Modifications in Antisense Research", Ed.
Y. S. Sanghui and P. Dan Cook. Nucleic acids containing one or more
carbocyclic sugars are also included within the definition of
nucleic acids (see Jerkins et al., Chem. Soc. Rev. (1995) pp. 169
176). Several nucleic acid analogs are described in Rawls, C &
E News Jun. 2, 1997 page 35. All of these references are hereby
expressly incorporated by reference. These modifications of the
ribose-phosphate backbone may be done to facilitate the addition of
additional moieties such as labels, or to increase the stability
and half-life of such molecules in physiological environments.
[0184] As will be appreciated by those in the art, all of these
nucleic acid analogs may find use in the present invention. In
addition, mixtures of naturally occurring nucleic acids and analogs
can be made. Alternatively, mixtures of different nucleic acid
analogs, and mixtures of naturally occurring nucleic acids and
analogs may be made.
[0185] Particularly preferred are peptide nucleic acids (PNA) which
includes peptide nucleic acid analogs. These backbones are
substantially non-ionic under neutral conditions, in contrast to
the highly charged phosphodiester backbone of naturally occurring
nucleic acids.
[0186] The nucleic acids may be single stranded or double stranded,
as specified, or contain portions of both double stranded or single
stranded sequence. The nucleic acid may be DNA, both genomic and
cDNA, RNA or a hybrid, where the nucleic acid contains any
combination of deoxyribo- and ribo-nucleotides, and any combination
of bases, including uracil, adenine, thymine, cytosine, guanine,
inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc. As
used herein, the term "nucleoside" includes nucleotides and
nucleoside and nucleotide analogs, and modified nucleosides such as
amino modified nucleosides. In addition, "nucleoside" includes
non-naturally occurring analog structures. Thus for example the
individual units of a peptide nucleic acid, each containing a base,
are referred to herein as a nucleoside.
[0187] As described above generally for proteins, nucleic acid
candidate modulator may be naturally occurring nucleic acids,
random nucleic acids, or "biased" random nucleic acids. For
example, digests of procaryotic or eucaryotic genomes may be used
as is outlined above for proteins. Where the ultimate expression
product is a nucleic acid, at least 10, preferably at least 12,
more preferably at least 15, most preferably at least 21 nucleotide
positions need to be randomized, with more preferable if the
randomization is less than perfect. Similarly, at least 5,
preferably at least 6, more preferably at least 7 amino acid
positions need to be randomized; again, more are preferable if the
randomization is less than perfect.
[0188] In a preferred embodiment, the candidate modulators are
organic moieties. In this embodiment, as is generally described in
WO 94/24314, candidate agents are synthesized from a series of
substrates that can be chemically modified. "Chemically modified"
herein includes traditional chemical reactions as well as enzymatic
reactions. These substrates generally include, but are not limited
to, alkyl groups (including alkanes, alkenes, alkynes and
heteroalkyl), aryl groups (including arenes and heteroaryl),
alcohols, ethers, amines, aldehydes, ketones, acids, estersramides,
cyclic compounds, heterocyclic compounds (including purines,
pyrimidines, benzodiazepins, beta lactams, tetracylines,
cephalosporins, and carbohydrates), steroids (including estrogens,
androgens, cortisone, ecodysone, etc.), alkaloids (including
ergots, vinca, curare, pyrollizdine, and mitomycines),
organometallic compounds, hetero atom bearing compounds, amino
acids, and nucleosides. Chemical (including enzymatic) reactions
may be done on the moieties to form new substrates or candidate
agents which can then be tested using the present invention.
[0189] As will be appreciated by those in the art, it is possible
to screen more than one type of candidate modulator at a time.
Thus, the library of candidate modulators used may include only one
type of agent (i.e., peptides), or multiple types (peptides and
organic agents). The assay of several candidates at one time is
further discussed below.
[0190] The present invention provides methods and compositions
comprising combining several components. In a preferred embodiment,
a preferred combination is tag-ubiquitin, E1, E2, and E3.
Preferably the tag is a label, a partner of a binding pair, or a
substrate binding molecule. More preferably, the tag is a
fluorescent label or a binding pair partner. In a preferred
embodiment, the tag is a binding pair partner and the ubiquitin is
labeled by indirect labeling. In the indirect labeling embodiment,
preferably the label is a fluorescent label or a label enzyme. In
an embodiment comprising a label enzyme, preferably the substrate
for that enzyme produces a fluorescent product. In a preferred
embodiment, the label enzyme substrate is luminol. In a preferred
embodiment, combining specifically excludes combining the
components with a target protein.
[0191] In another preferred embodiment, a preferred combination is
Tag1-ubiquitin, tag2-ubiquitin, E1, E2 and E3. Preferably, tag1 and
tag2 are labels, preferably fluorescent labels, most preferably
tag1 and tag2 constitute a FRET pair.
[0192] In a preferred embodiment, a preferred combination is
tag1-ubiquitin, E1, E2 and tag2-E3. Preferably, tag1 is a label, a
partner of a binding pair, or a substrate binding molecule and tag2
is a different label, partner of a binding pair, or substrate
binding molecule. More preferably, tag1 is a fluorescent label or a
member of a binding pair. When tag1 is a member of a binding pair,
preferably tag1 is indirectly labeled. Still more preferably, tag-1
is indirectly labeled with a label enzyme. Preferably the label
enzyme substrate used to reveal the presence of the enzyme produces
a fluorescent product, and more preferably is luminol. In the
presently described combination, preferably tag2 is a surface
substrate binding element, more preferably a His-tag.
[0193] In a preferred embodiment, a preferred combination is
tag1-ubiquitin, E1 and tag2-E2. In this embodiment, preferably,
tag1 is a label, a partner of a binding pair, or a substrate
binding molecule and tag2 is a different label, partner of a
binding pair, or substrate binding molecule. More preferably, tag-1
is a label or a member of a binding pair. When tag1 is a member of
a binding pair, preferably tag1 is indirectly labeled. In a
preferred embodiment, the tag1 label (direct or indirect) is a
fluorescent label or a label enzyme. When the tag1 label (direct or
indirect) is a label enzyme, preferably the reaction substrate used
to reveal the presence of the enzyme produces a fluorescent
product, and more preferably is luminol. In the presently described
combination, preferably tag2 is a substrate binding element, more
preferably a His-tag.
[0194] In a preferred embodiment, the compositions of the invention
do not comprise a target protein. In this embodiment, ubiquitin is
the sole ubiquitination substrate, as discussed above. This
embodiment stands in contrast to previous ubiquitination enzyme
assays, which required addition of a target protein as part of the
composition. Because the different combinations of E3 and E2 and
combinations of E3 subunits are specific to particular target
proteins, the present assays are much more versatile, allowing any
variation of such combinations without first identifying the
specific target protein to which the combination is directed.
[0195] The components of the present compositions may be combined
in varying amounts. In a preferred embodiment, ubiquitin is
combined at a final concentration of from 20 to 200 ng per 100
.mu.l reaction solution, most preferable at about 100 ng per 100
.mu.l reaction solution.
[0196] In a preferred embodiment, E1 is combined at a final
concentration of from 1 to 50 ng per 100 .mu.l reaction solution,
more preferably from 1 ng to 20 ng per 100 .mu.l reaction solution,
most preferably from 5 ng to 10 ng per 100 .mu.l reaction
solution.
[0197] In a preferred embodiment, E2 is combined at a final
concentration of 10 to 100 ng per 100 .mu.l reaction solution, more
preferably 10-50 ng per 100 .mu.l reaction solution.
[0198] In a preferred embodiment, E3 is combined at a final
concentration of from 1 ng to 500 ng per 100 .mu.l reaction
solution, more preferably from 50 to 400 ng per 100 .mu.l reaction
solution, still more preferably from 100 to 300 ng per 100 .mu.l
reaction solution, most preferably about 100 ng per 100 .mu.l
reaction solution.
[0199] The components of the invention are combined under reaction
conditions that favor ubiquitin ligase activity and/or
ubiquitination activity. Generally, this will be physiological
conditions. Incubations may be performed at any temperature which
facilitates optimal activity, typically between 4 and 40.degree. C.
Incubation periods are selected for optimum activity, but may also
be optimized to facilitate rapid high through put screening.
Typically between 0.5 and 1.5 hours will be sufficient.
[0200] A variety of other reagents may be included in the
compositions. These include reagents like salts, solvents, buffers,
neutral proteins, e.g. albumin, detergents, etc. which may be used
to facilitate optimal ubiquitination enzyme activity and/or reduce
non-specific or background interactions. Also reagents that
otherwise improve the efficiency of the assay, such as protease
inhibitors, nuclease inhibitors, anti-microbial agents, etc., may
be used. The compositions will also preferably include adenosine
triphosphate (ATP).
[0201] The mixture of components may be added in any order that
promotes ubiquitin ligase activity or optimizes identification of
candidate modulator effects. In a preferred embodiment, ubiquitin
is provided in a reaction buffer solution, followed by addition of
the ubiquitination enzymes. In an alternate preferred embodiment,
ubiquitin is provided in a reaction buffer solution, a candidate
modulator is then added, followed by addition of the ubiquitination
enzymes.
[0202] Once combined, preferred methods of the invention comprise
measuring the amount of ubiquitin bound to E3. In an alternate
preferred embodiment in which the combination lacks E3, preferred
methods of the invention comprise measuring the amount of ubiquitin
bound to E2. As will be understood by one of ordinary skill in the
art, the mode of measuring will depend on the specific tag attached
to the ubiquitin. As will also be apparent to the skilled artisan,
the amount of ubiquitin bound will encompass not only the
particular ubiquitin protein bound directly to the ubiquitination
enzyme, but also the ubiquitin proteins bound to that particular
ubiquitin in a polyubiquitin chain.
[0203] In a preferred embodiment, the tag attached to the ubiquitin
is a fluorescent label. In a preferred embodiment, the tag attached
to ubiquitin is an enzyme label or a binding pair member which is
indirectly labeled with an enzyme label. In this latter preferred
embodiment, the enzyme label substrate produces a fluorescent
reaction product. In these preferred embodiments, the amount of
ubiquitin bound is measured by luminescence.
[0204] As used herein, "luminescence" or "fluorescent emission"
means photon emission from a fluorescent label. In an embodiment
where FRET pairs are used, fluorescence measurements may be taken
continuously or at time points during the ligation reaction.
Equipment for such measurement is commercially available and easily
used by one of ordinary skill in the art to make such a
measurement.
[0205] Other modes of measuring bound ubiquitin are well known in
the art and easily identified by the skilled artisan for each of
the labels described herein. For instance, radioisotope labeling
may be measured by scintillation counting, or by densitometry after
exposure to a photographic emulsion, or by using a device such as a
PhosphorImager. Likewise, densitometry may be used to measure bound
ubiquitin following a reaction with an enzyme label substrate that
produces an opaque product when an enzyme label is used.
[0206] In preferred methods of the present invention, E3 is bound
to a surface substrate. This may be done directly, as described
above for the binding of a label to ubiquitin. This may also be
accomplished using tag E3, wherein the tag is a surface substrate
binding molecule.
[0207] In another preferred embodiment of the invention, E2 is
bound to a surface substrate in the absence of E3. This may be done
directly, as described above for the binding of a label to
ubiquitin. This may also be accomplished using tag-E2, wherein the
tag is a surface substrate binding molecule.
[0208] In the two preferred embodiments described immediately
above, E3 and E2 are in the form of tag-E3 and tag-E2,
respectively, and are bound to a surface substrate via a surface
substrate binding molecule tag. In general, any substrate binding
molecule can be used. In a preferred embodiment, the tag is a
His-tag and the surface substrate is nickel. In a preferred
embodiment, the nickel surface substrate is present on the surface
of the wells of a multi-well plate, such as a 96 well plate. Such
multi-well plates are commercially available. The binding of the
enzyme to a surface substrate facilitates the separation of bound
ubiquitin from unbound ubiquitin. In the present embodiment, the
unbound ubiquitin is easily washed from the receptacle following
the ligation reaction. As will be appreciated by those of skill in
the art, the use of any surface substrate binding element and
receptacle having the surface substrate to which it binds will be
effective for facilitating the separation of bound and unbound
ubiquitin.
[0209] In an alternative embodiment, E3 or E2 is bound, directly or
via a substrate binding element, to a bead. Following ligation, the
beads may be separated from the unbound ubiquitin and the bound
ubiquitin measured. In a preferred embodiment, E3 or E2 is bound to
beads and the composition used includes tag-ubiquitin wherein tag
is a fluorescent label. In this embodiment, the beads with bound
ubiquitin may be separated using a fluorescence activated cell
sorting (FACS) machine. Methods for such use are described in U.S.
patent application Ser. No. 09/047,119, which is hereby
incorporated in its entirety. The amount of bound ubiquitin can
then be measured.
[0210] In another embodiment, none of the ubiquitination enzymes is
bound to a substrate. Preferably in this embodiment, the
composition comprises tag1-ubiquitin, tag2-ubiquitin, E1, E2 and
E3. Preferably, tag1 and tag2 are labels, preferably fluorescent
labels, most preferably tag1- and tag2 constitute a FRET pair. In
this embodiment, ubiquitination is measured by measuring the
fluorescent emission spectrum. This measuring may be continuous or
at one or more times following the combination of the components.
Alteration in the fluorescent emission spectrum of the combination
as compared with unligated ubiquitin indicates the amount of
ubiquitination. The skilled artisan will appreciate that in this
embodiment, alteration in the fluorescent emission spectrum results
from ubiquitin bearing different members of the FRET pair being
brought into close proximity, either through the formation of
poly-ubiquitin and/or by binding nearby locations on a protein,
preferably a target protein.
[0211] In a preferred embodiment, the compositions of the invention
are used to identify ubiquitination modulators. In this embodiment,
the composition includes a candidate modulator. In a preferred
embodiment, the measured amount and/or rate of tag-ubiquitin
binding to E3 is compared with the that when the candidate
modulator is absent from the composition, whereby the presence or
absence of the modulators effect on ubiquitin ligase activity is
determined. In this embodiment, whether the modulator enhances or
inhibits ubiquitination is also determined.
[0212] In a preferred embodiment, the composition of the invention
containing a candidate modulator lacks E3 and the amount and/or
rate of ubiquitin binding to E2 is measured. This embodiment may
also comprise the step of comparing the amount and/or rate of
ubiquitin binding to E2 in a composition lacking both E3 and the
candidate modulator, whereby the modulatory activity of the
candidate on ubiquitination enzymes other than E3 is determined. In
a preferred embodiment, the percentage difference in the amount of
ubiquitin bound to E2 in the presence and absence of the candidate
modulator is compared with the percentage difference in the amount
bound to E3 in the presence and absence of candidate modulator,
whereby the point of effect of the candidate modulator in the
enzyme cascade is determined. That is, it is determined whether the
candidate modulator affects E3 ubiquitin ligase activity or it
affects E1 ubiquitin activating activity and/or E2 ubiquitin
conjugating activity.
[0213] In another preferred embodiment, the compositions of the
invention are used to identify ubiquitination modulators. In this
embodiment, the composition includes a candidate modulator. In a
preferred embodiment, where tag1 and tag2 constitute a FRET pair,
the measured amount and/or rate of tag1-ubiquitin and
tag2-ubiquitin binding to a substrate protein (as poly-ubiquitin
and/or ubiquitin bound to a target protein) is compared with the
amount or rate of such binding in the absence of the candidate
modulator, whereby the presence or absence of the modulator's
effect on ubiquitin ligase activity is determined. In this
embodiment, whether the modulator enhances or inhibits
ubiquitination is also determined.
[0214] In a preferred embodiment, multiple assays are performed
simultaneously in a high throughput screening system. In this
embodiment, multiple assays may be performed in multiple
receptacles, such as the wells of a 96 well plate or other
multi-well plate. As will be appreciated by one of skill in the
art, such a system may be applied to the assay of multiple
candidate modulators and/or multiple combination of E3 components
and/or E2-E3 pairings. In a preferred embodiment, the present
invention is used in a high throughput screening system for
determining the ubiquitin ligase activity of different E2-E3
pairings and/or different E3 component combinations. In an
alternate preferred embodiment, the present invention is used in a
high throughput screening system for simultaneously testing the
effect of individual candidate modulators.
[0215] In another aspect, the invention provides a method of
assaying for ubiquitination activity or ubiquitination enzyme
activity in a mixture. Ubiquitin is introduced into a cell or
mixture of protein, preferably a cell lysate, under conditions in
which ubiquitination can take place. In this embodiment, the
ubiquitin is in the form of tag1-ubiquitin and tag2-ubiquitin,
wherein tag1 and tag2 constitute a FRET pair or tag1 is a
fluorescent label and tag2 is a quencher of tag1. Fluorescent
emission spectrum is measured as an indication of whether
ubiquitination activity is present in the mixture or cell. In a
preferred embodiment, the ubiquitin also comprises a member of a
binding pair, such as FLAG (DYKDDDDK; SEQ ID NO: 16). In this
latter embodiment, components involved in ubiquitination can be
isolated from the mixture using any one of a number of affinity
based separation means such as fluorescent beads coated with
anti-FLAG (DYKDDDDK; SEQ ID NO:16) antibody or amino precipitation
using anti-FLAG (DYKDDDDK; SEQ ID NO: 16) antibodies, or using
anti-FLAG (DYKDDDDK; SEQ ID NO: 16) antibody attached to a solid
support. Other means of separating ubiquitin bound components of
the cell or mixture will be readily apparent to the skilled
artisan. Ubiquitin bound components so separated in this method may
include E3 and target protein. The skilled artisan will appreciate
that separation of these components for individual identification
or subsequent investigation may be obtained by several means well
known in the art, such as by HPLC or electrophoresis.
[0216] It is understood by the skilled artisan that the steps of
the assays provided herein can vary in order. It is also
understood, however, that while various options (of compounds,
properties selected or order of steps) are provided herein, the
options are also each provided individually, and can each be
individually segregated from the other options provided herein.
Moreover, steps which are obvious and known in the art that will
increase the sensitivity of the assay are intended to be within the
scope of this invention. For example, there may be additionally
washing steps, blocking steps, etc.
[0217] The following examples serve to more fully describe the
manner of using the above-described invention, as well as to set
forth the best modes contemplated for carrying out various aspects
of the invention. It is understood that these examples in no way
serve to limit the true scope of this invention, but rather are
presented for illustrative purposes. All references cited herein
are expressly incorporated by reference in their entirety.
EXAMPLES
Example 1
Production of E2, E3 and Ubiquitin
E2 Production
[0218] The open reading frame of E2 (Ubc5C) was amplified by PCR
and cloned into the pGex-6p-1 E. Coli. expression vector (Amersham
Pharmacia) as Bg1II-EcoRI fragments, with N-terminus in frame fused
to the GST tag.
Materials and Methods
[0219] Plasmid is transformed in BL21 DE3 competent E. coli
(Stratagene, cat #230132). Cells are grown at 37.degree. C. in
TB+100 ug/ml ampicillin and 0.4% glucose to an OD600 of about 0.6,
induced with addition of 320 uM IPTG and allowed to grow for
another 3 h before harvest. The pellets are washed once with cold
PBS, then resuspended in about 6 volumes of lysis buffer (20 mM
Tris, 10% glycerol, 0.5 M Nacl, 2.5 mM EDTA, 1 mM TCEP plus
Complete-EDTA Free Protease inhibitor tablets, 1 tablet/25 ml of
resuspended cells, pH 8.0). The suspension is homogenized and
sonicated 3.times.30 sec. NP40, then added to a final concentration
of 0.5% and the tubes are rocked for 30 min at 4.degree. C.
Following centrifugation at 11000 rpm for 25 to 30 min, the
supernatant is incubated with Glutathione Sepharose 4B (Amersham,
cat #17-0756-01) at a ratio of 1 ml of beads per 100 ml of original
culture volume for 1 to 2 hours at 4.degree. C. with gentle
rocking. The beads are pelleted and washed once with 10 bed volumes
of the lysis buffer, then twice with 10 bed volumes of Prescission
Protease buffer (50 mM Tris HCL, 150 mM NaCl, 1 mM EDTA, 1 mM DTT,
0.1% NP-40, pH 7.0.). Prescission Protease (Amersham, product #
27-0843) is added at a ratio of 80 ul (160 Units) per ml of
GST-resin, and allowed to incubate for 4 h at 4.degree. C. The
supernatant containing the cleaved E2 protein is collected, and the
resin is washed twice with one bed volume of Prescission buffer.
All three fractions are analyzed by SDS-PAGE and pooled when
appropriate.
Ubiquitin Production
[0220] Ubiquitin was cloned into the pFlag-Mac Expression Vector
(Sigma) as a HindIII-EcoRI fragment by PCR. This results in
expression of amino-terminal FLAG (DYKDDDDK; SEQ ID NO: 16) fusion
ubiquitin in E. coli.
Materials and Methods
[0221] The induction of protein expression and cell lysis is
similar to the above GST-E2 preparation, except that the
supernatant is loaded over a FLAG (DYKDDDDK; SEQ ID NO:
16)-affinity resin (VWR, cat #IB 13020) at a ratio of 15 ml of
beads per IL of original culture. The resin is then washed with 10
bed volumes of lysis buffer. The protein is eluted from the column
with: 100 mM Acetic acid, 10% glycerol, 200 mM NaCl, 2.5 mM EDTA,
0.1% NP-40, pH 3.5. The elutions are collected as 1 bed volume
fractions into tubes that contain 1/10th volume of 2M Tris, 80 mM
B-ME, pH 9.0 to neutralize the pH. The elution fractions are
analyzed by SDS-PAGE and the appropriate fractions are pooled and
dialyzed against 400 volumes of 20 mM Tris, 10% glycerol, 200 mM
NaCl, 2.5 mM EDTA, pH 8.0.
Production of E3
[0222] Coding sequences for E3 complex were also amplified by PCR
and baculoviruses were generated using the Bac-to-Bac system
(GibcoBRL). E3 contains two subunits, which are expressed by
co-infection of the two baculovirus in the same Hi-5 insect cells.
One of the subunit is His-tagged, with the other associating
subunit untagged.
[0223] The detail procedure was done following the Bac to Bac
Baculovirus Expression system by GibcoBRL. For example, ROC1 was
cloned into the pFastBacHtb vector with a N-terminal His6 (SEQ ID
NO:21) tag, while CUL1 was inserted into the pFastBac1 vector
without any fusing tag. After transposition and Bacmid DNA
transfection into SF-9 cells, Baculoviruses were harvested,
amplified, and used to co-infect Hi-5 cells for protein
expression.
Materials and Methods
[0224] Cells are harvested, washed once with cold PBS, and
resuspended in about 6 volumes of lysis buffer (20 mM Tris, 20%
glycerol, 0.5 M Nacl, 15 mM imidazole, 1 mM TCEP plus Complete-EDTA
Free Protease inhibitor tablets, 1 tablet/25 ml of resuspended
cells, pH 8.0.). The suspension is then sonicated 3.times.30 sec,
followed by addition of NP40 to a final concentration of 0.5% and
incubation for 30 min at 4.degree. C. The lysate is then
centrifuged and the supernatant is incubated with pre-equilibrated
(lysis buffer+NP40) Ni-NTA Agarose beads (Qiagen, cat #1000632) for
1 to 2 hrs. The pelleted beads are washed 2 times with lysis
buffer, resuspended in 1 to 2 volumes of lysis buffer and
transferred to a disposable column for elution. Elution is
accomplished using 5.times.1-bed volume aliquots of Lysis
buffer+250 mM imidazole. Elution fractions are analyzed by SDS-PAGE
and appropriate fractions are pooled. The elution pool is then
desalted using either a desalting column or a centrifugal
concentration device (more often used for large volumes.) When
using centrifugal devices, the eluted pool is diluted 1:1 with
lysis buffer that has no imidazole and spun at the appropriate
speed until the volume is reduced by half. At this point an equal
volume of fresh buffer is added and the device is respun. This is
done a total of four times resulting in a 32 fold exchange.
Example 2
Ubiquitin Conjugation Assay
[0225] Ubiquitin conjugating activity of E1+E2 was measured using
the following protocol with FLAG (DYKDDDDK; SEQ ID NO: 16)-ubiquin,
purified from E. Coli, and the E2 Ubch5c, purified as His-Ubch5c
from E. Coli.
Materials and Methods
[0226] The following procedures were used for assays measuring
ubiquitin conjugation. The wells of Nickel substrate 96-well plates
(Pierce Chemical) are blocked with 100 .mu.l of 1% casein/phosphate
buffered saline (PBS) for 1 hour at room temperature, then washed
with 200 .mu.l of PBST (0.1% Tween-20 in PBS) 3 times. To each well
is added the following FLAG-ubiquitin (SEQ ID NO: 14) (see above)
reaction solution:
Final Concentration
62.5 mM Tris pH 7.5
6.25 mM MgCl.sub.2
0.75 mM DTT
2.5 mM ATP
2.5 mM NaF
[0227] 12.5 nM Okadaic acid 100 ng FLAG-ubiquitin (SEQ ID NO: 14)
(made as described above).
[0228] The buffer solution is brought to a final volume of 80 .mu.l
with Millipore-filtered water, followed by the addition of 10 .mu.l
of DMSO.
[0229] To the above solution is then added 10 .mu.l of E1, His-E2
in 20 mM Tris buffer, pH 7.5, and 5% glycerol. His-E2 is made as
described above. E1 is obtained commercially (Affiniti Research
Products, Exeter, U.K.). The following amounts of each enzyme are
used for these assays: 5 ng/well of E1; 25 nl/well E2. The reaction
is then allowed to proceed at room temperature for 1 hour.
[0230] Following the ubiquitin conjugation reaction, the wells are
washed with 200 .mu.l of PBST 3 times. For measurement of the
enzyme bound ubiquitin, 100 .mu.l of Mouse anti-FLAG (DYKDDDDK; SEQ
ID NO:16) (1:10,000) and anti-Mouse Ig-HRP (1:15,000) in PBST are
added to each well and allowed to incubate at room temperature for
1 hour. The wells are then washed with 200 .mu.l of PBST 3 times,
followed by the addition of 100 .mu.l of luminal substrate (1/5
dilution). Luminescence for each well is then measured using a
fluorimeter.
Results
Ubiquitin Activating and Conjugating Activity
[0231] FIG. 1A shows the luminescence measured for E1 alone and for
E1+his-E2, as described above.
Example 3
Ubiquitin Ligase Assay
[0232] Ubiquitin ligase activity of E1+E2+E3 was measured using the
following protocol with FLAG-ubiquin (SEQ ID NO: 14), purified from
E. Coli, the E2 UbchSc, purified as GST-UbchSc from E. Coli with
the GST tag removed, and the E3 His-ROC/Cul 1 complex purified from
Hi-5 cells by Baculovirus co-infection. This assay was also used to
show the effects of candidate modulators on ubiquitin ligase
activity.
Materials and Methods
[0233] The wells of Nickel-substrate 96-well plates (Pierce
Chemical) are blocked with 100 .mu.l of 1 casein/phosphate buffered
saline (PBS) for 1 hour at room temperature, then washed with 200
.mu.l of PBST (0.1% Tween-20 in PBS) 3 times. To each well is added
the following FLAG-ubiquitin (SEQ ID NO: 14) (see above) reaction
solution:
Final Concentration
62.5 mM Tris pH 7.5
6.25 mM MgCl.sub.2
0.75 mM DTT
2.5 mM ATP
2.5 mM NaF
[0234] 12.5 nM Okadaic acid 100 ng FLAG-ubiquitin (SEQ ID NO: 14)
(made as described above).
[0235] The buffer solution is brought to a final volume of 80 pl
with Millipore-filtered water.
[0236] For assays directed to identifying modulators of ubiquitin
ligase activity, 10 .mu.l of a candidate modulator compound in DMSO
is then added to the solution. If no candidate modulator is added,
10 .mu.l of DMSO is added to the solution.
[0237] To the above solution is then added 10 .mu.l of
ubiquitination enzymes in 20 mM Tris buffer, pH 7.5, and 5%
glycerol. E2-UbchSc and E3-His ROC1/Cul1 are made as described
above. E1 is obtained commercially (Affiniti Research Products,
Exeter, U.K.). The following amounts of each enzyme are used for
these assays: 5 ng/well of E1; 25 nl/well E2; and 100 ng/well
His-E3. The reaction is then allowed to proceed at room temperature
for 1 hour.
[0238] Following the ubiquitination reaction, the wells are washed
with 200 .mu.l of PBST 3 times. For measurement of the enzyme bound
ubiquitin, 100 .mu.l of Mouse anti-FLAG (DYKDDDDK; SEQ ID NO:16)
(1:10,000) and anti-Mouse Ig HRP (1:15,000) in PBST are added to
each well and allowed to incubate at room temperature for 1 hour.
The wells are then washed with 200 .mu.l of PBST 3 times, followed
by the addition of 100 .mu.l of luminol substrate (1/5 dilution).
Luminescence for each well is then measured using a
fluorimeter.
Results
Ubiquitin Ligase Activity
[0239] FIG. 1 shows the luminescence measured for several different
combinations of ubiquitination enzymes. In these experiments, only
E3 was in the form His-E3. The luminescence measurements show that
the assay specifically measures the activity of the entire
ubiquitination enzyme cascade, which requires the presence of all
three ubiquitination enzymes in the reaction.
Variations of Composition Components
[0240] FIG. 2A shows the relative effect of varying the amount of
E1 on ubiquitin ligase activity in the above procedure, in presence
and absence of DMSO. The addition of about 10 ng per 100 .mu.l
reaction solution provides maximum ubiquitin ligase activity with
the other components of the composition kept as detailed above. The
presence of DMSO does not significantly affect the activity of the
ubiquitination enzymes.
[0241] The relative effect of varying E3 and ubiquitin
concentration of the reaction composition is shown in FIG. 2B.
Generally speaking, maximum ubiquitin ligase activity was obtained
with 200 to 300 ng per 100 .mu.l of E3 at each concentration of
ubiquitin, while increasing ubiquitin concentration generally
increased ubiquitin ligase activity at each concentration of
E3.
[0242] It was also found that blocking of the wells with 1% casein
improved the signal to noise ratio over either no blocking or
blocking with 5% bovine serum albumen (BSA). Background was
determined after combining all of the components as above except
His-E3 and measuring the resulting fluorescence after pre-treating
the wells with 5% BSA, 1% casein or nothing. Results are shown in
FIG. 3.
Identification of Modulators of Ubiquitin Ligase Activity
[0243] To show that the assay is useful for identifying modulators
of ubiquitin ligase activity, several candidate modulators were
combined at varying concentrations with the assay components as
described above. FIG. 4 shows the results from two identified
modulators of ubiquitin ligase activity. The modulators decreased
ubiquitin ligase activity in a dose-dependent fashion for
ubiquitination enzyme compositions comprising either ROC1/Cul1 or
ROC2/Cul5 as the E3 component.
[0244] Comparison of the effect of ubiquitin ligase activity
modulators on reaction compositions, as described above, either
containing E1, E2 and His-E3 or containing E1, His-E2 and lacking
E3 shows whether the modulator affects E3 or an enzyme other than
E3. In FIG. 5A, the identified modulator decreases ubiquitin ligase
activity in the presence of E3, but does not alter activity in the
absence of E3, showing that the modulator has a specific effect on
E3 ligase activity. In contrast, results shown in FIG. 5B for
another modulator reveals that this compound reduces activity
whether or not E3 is present, showing that this modulator affects a
member of the ubiquitination enzyme cascade other than E3.
Example 4
FRET Analysis of Ligated Ubiquitin
[0245] Ubiquitin was prepared, labeled with either EDANS or
fluorescein, and the fluorescence of each of these labels and their
interaction as a FRET pair was measured to show binding of the
labeled ubiquitin to E3 and FRET activity in the bound
ubiquitin.
Materials and Methods
[0246] Ubiquitin were produced incorporating Cys residues into the
Flag-ubiquitin (SEQ ID NO: 14) sequence by site directed
mutagenesis using either the primer
TABLE-US-00002 (SEQ ID NO: 19)
5'-CCCCCCAAGCTTTGCATGCAGATTTTCGTGAAGACCCTGACC-3'
to produce Flag-Cys-ubiquitin (SEQ ID NO: 15), or the primer
TABLE-US-00003 (SEQ ID NO: 20)
5'-CCCCCCAAGCTTGCGTGCATGCAGATTTTCGTGAAGACCCTGACC- 3'
to produce FLAG-Ala-Cys-ubiquitin (SEQ ID NO: 18). Protein was
expressed and purified as described above.
[0247] Either fluoresceine 5-maleimide (peak emission at 515 nm) or
1,5-iodacetamide EDANS (IAEDANS; peak emission at 490 nm) was
reacted with the thiol group on the cysteine of the ubiquitin
produced as above to form a thioether. The labeling was performed
in PBS with 1 mM TCEP. Labeled protein was separated from free
label by gel filtration.
[0248] Ubiquitin ligase assay was performed substantially as
described above, with a few modifications. no nickel substrate was
used in the reaction wells, so all of the components were free in
solution. Equal amounts of fluoresceine labeled ubiquitin and
IAEDANS labeled ubiquitin were used. The reaction was performed at
room temperature for 2 hours in a volume of 100-150 .mu.l, then
stopped with 50 .mu.l of 0.5M EDTA, pH 8.
[0249] Following the reaction, the products were separated in PBS
with 1 mM TCEP by HPLC on a Superdex-75 HR 10/30 size-exclusion
column using fluorescence emission detection. A larger molecular
weight cutoff gel-filtration column (e.g., Superdex 200 HR 10/30)
could be used to resolve individual ligation species.
Results
[0250] Fluoresceine labeled ubiquitin and IAEDANS labeled ubiquitin
was bound to E3 in approximately equal amounts. A comparison of the
spectral analysis of fluorescent emission from the free (unligated)
ubiquitin labeled with both fluorophores and the E3-bound ubiquitin
shows a distinct increase in ratio of emission at 515 nm versus 490
nm (FIG. 17). This shows that in ligated ubiquitin, the fluorphores
on different ubiquitin molecules are sufficiently close for FRET to
be measured.
Sequence CWU 1
1
2113177DNAOryctolagus cuniculusrabbit E1 1atgtccagct cgccgctgtc
caagaaacgt cgcgtgtccg ggcctgatcc aaagccgggt 60tctaactgct cccctgccca
gtccgtgttg ccccaagtgc cctcggcgcc aaccaacgga 120atggcgaaga
acggcagtga agcagacatc gatgagggcc tttactcccg gcagctgtat
180gtgttgggcc atgaggcgat gaagcggctc cagacatcca gcgttctggt
gtcaggcctg 240cggggcctgg gggtagagat cgcgaagaac atcatccttg
gcggggtcaa ggccgtgacc 300ctccatgacc agggcacggc ccagtgggct
gacctctcct cccagttcta cctgcgagag 360gaggacatag ggaaaaaccg
cgctgaggtg tcacagcccc gccttgctga actcaatagc 420tacgtgcctg
tcaccgccta cactgggccg ctggttgagg acttcctcag tggcttccag
480gtggtggtcc tcactaacag ccccctggag gaccagctgc gcgtgggcga
gttctgtcat 540agccgtggca tcaagctggt agtggcagac acgagaggct
tgtttgggca actcttctgc 600gactttggag aggaaatgat cctcacagat
tccaacgggg agcagcccct cagcaccatg 660gtttctatgg tcaccaagga
caaccctggt gtggttacct gcctggatga ggcccgacat 720gggtttgaga
gtggcgattt tgtttccttc tccgaagtac agggcatgac tgagctcaat
780ggaaaccagc ccatagagat caaagtcctg ggtccttaca cctttagcat
ctgtgacacc 840tccaacttct ccgattacat ccgtggaggc attgtcagcc
aggtcaaagt acctaagaag 900ataagcttta aatccttgtc agcctcgctg
gcagagcctg actttgtgat gacggacttc 960gccaagtttt ctcgccccgc
tcagcttcac attggcttcc aggccttgca caagttctgt 1020gcacagcaca
gccggccacc tagaccccgg aacgaggagg atgcagcaga gctggtgacc
1080ctagcacgcg ctgtgaactc taaagcctcg tcggcagtgc agcaagatag
cctggatgag 1140gacctcatcc ggaacctggc ctttgtggca gccggggacc
tggcgcccat caatgccttc 1200attgggggcc tggctgccca ggaagtcatg
aaggcctgct ctgggaagtt tatgcccatc 1260atgcagtggc tgtactttga
tgcccttgag tgtctcccgg aggacaaaga atccctcaca 1320gaggacaagt
gcctcccgcg ccagaaccgt tatgatgggc aggtggctgt gtttggctca
1380gacctgcaag agaagctggg caggcagaag tacttcctgg tgggtgcagg
ggctattggc 1440tgtgagctgc tcaagaactt tgccatgatt gggctgggct
gtggtgagaa cggagaaata 1500attgtcacag acatggacac cattgagaaa
tctaatctga accgacagtt tctattccgg 1560ccctgggatg tcacgaagtt
aaaatctgac acagctgctg cagctgtgca ccagatgaat 1620ccacatatcc
gggtgacaag ccaccagaac cgtgtgggtc ctgacactga acgtatctac
1680gacgacgatt tcttccaaac tctggatggc gtggccaacg ccttagacaa
cgtggatgcc 1740cgcatgtaca tggaccgccg ctgcgtgtac taccggaagc
cgctgctcga atcaggcacc 1800ctgggcacca agggcaacgt ccaggtggtg
atccccttcc tgacagagtc ctacagctcc 1860agccaagacc cacctgagaa
gtccatcccc atctgtaccc tgaagaactt ccccaacgcc 1920atcgaacaca
ctcttcagtg ggctcgggat gaatttgaag gcctcttcaa gcagccagcg
1980gaaaatgtca accagtacct cacagaccct aagtttgtgg agcggacatt
gcggctggcg 2040ggtacccagc cactggaggt gctggaggct gtgcagcgca
gcctggtgct gcagctaccg 2100cagagctggg cagactgtgt gacctgggcc
tgccaccact ggcacaccca gtattctaac 2160aatatccggc agctgttgca
caacttccct cccgaccagc tcacaagctc gggagctccc 2220ttctggtctg
ggcccaaacg ttgtcctcac ccactcacct ttgatgttag caaccctctg
2280catctggact atgtgatggc tgctgccaac ctgtttgccc agacctacgg
gctggcaggc 2340tctcaggacc gagctgctgt ggccacactc ctgcagtctg
tacaggtccc cgagtttacc 2400cccaagtctg gcgtcaaaat ccacgtttct
gaccaggagc tgcagagcgc caatgcttct 2460gttgacgaca gccgtttaga
ggagctcaag gctacgctgc ctagccccga caagctccct 2520ggattcaaga
tgtaccccat tgactttgag aaggatgatg atagtaactt tcacatggac
2580ttcattgtgg ccgcatccaa cctccgggcc gaaaactatg acattccccc
tgcagaccgg 2640cacaagagca agctgattgc agggaagatc atcccagcca
ttgccacgac cacagcagct 2700gtcgttggcc ttgtgtgtct ggagctgtac
aaggtagtgc agggacaccg acacctcgac 2760tcctacaaga atggtttcct
caacctggcc ctgccgtttt tcggtttctc tgaacctctg 2820gctgcaccac
gtcaccagta ctataaccaa gagtggacat tgtgggatcg ctttgaggtt
2880cagggactgc agcccaacgg tgaggagatg accctcaaac aattcctcga
ctactttaag 2940acagagcaca aattggagat taccatgctg tcccagggtg
tgtccatgct ctattccttc 3000tttatgccag ctgcgaagct caaggaacgg
ttggaccagc cgatgacaga gattgtaagc 3060cgtgtgtcga agcgaaagct
gggccgccac gtgcgggcgc tggtgcttga gctgtgctgc 3120aacgacgaga
gcggcgagga cgtcgaagtc ccctacgtcc gatataccat ccgttaa
317721058PRTOryctolagus cuniculusrabbit E1 2Met Ser Ser Ser Pro Leu
Ser Lys Lys Arg Arg Val Ser Gly Pro Asp1 5 10 15Pro Lys Pro Gly Ser
Asn Cys Ser Pro Ala Gln Ser Val Leu Pro Gln 20 25 30Val Pro Ser Ala
Pro Thr Asn Gly Met Ala Lys Asn Gly Ser Glu Ala 35 40 45Asp Ile Asp
Glu Gly Leu Tyr Ser Arg Gln Leu Tyr Val Leu Gly His 50 55 60Glu Ala
Met Lys Arg Leu Gln Thr Ser Ser Val Leu Val Ser Gly Leu65 70 75
80Arg Gly Leu Gly Val Glu Ile Ala Lys Asn Ile Ile Leu Gly Gly Val
85 90 95Lys Ala Val Thr Leu His Asp Gln Gly Thr Ala Gln Trp Ala Asp
Leu 100 105 110Ser Ser Gln Phe Tyr Leu Arg Glu Glu Asp Ile Gly Lys
Asn Arg Ala 115 120 125Glu Val Ser Gln Pro Arg Leu Ala Glu Leu Asn
Ser Tyr Val Pro Val 130 135 140Thr Ala Tyr Thr Gly Pro Leu Val Glu
Asp Phe Leu Ser Gly Phe Gln145 150 155 160Val Val Val Leu Thr Asn
Ser Pro Leu Glu Asp Gln Leu Arg Val Gly 165 170 175Glu Phe Cys His
Ser Arg Gly Ile Lys Leu Val Val Ala Asp Thr Arg 180 185 190Gly Leu
Phe Gly Gln Leu Phe Cys Asp Phe Gly Glu Glu Met Ile Leu 195 200
205Thr Asp Ser Asn Gly Glu Gln Pro Leu Ser Thr Met Val Ser Met Val
210 215 220Thr Lys Asp Asn Pro Gly Val Val Thr Cys Leu Asp Glu Ala
Arg His225 230 235 240Gly Phe Glu Ser Gly Asp Phe Val Ser Phe Ser
Glu Val Gln Gly Met 245 250 255Thr Glu Leu Asn Gly Asn Gln Pro Ile
Glu Ile Lys Val Leu Gly Pro 260 265 270Tyr Thr Phe Ser Ile Cys Asp
Thr Ser Asn Phe Ser Asp Tyr Ile Arg 275 280 285Gly Gly Ile Val Ser
Gln Val Lys Val Pro Lys Lys Ile Ser Phe Lys 290 295 300Ser Leu Ser
Ala Ser Leu Ala Glu Pro Asp Phe Val Met Thr Asp Phe305 310 315
320Ala Lys Phe Ser Arg Pro Ala Gln Leu His Ile Gly Phe Gln Ala Leu
325 330 335His Lys Phe Cys Ala Gln His Ser Arg Pro Pro Arg Pro Arg
Asn Glu 340 345 350Glu Asp Ala Ala Glu Leu Val Thr Leu Ala Arg Ala
Val Asn Ser Lys 355 360 365Ala Ser Ser Ala Val Gln Gln Asp Ser Leu
Asp Glu Asp Leu Ile Arg 370 375 380Asn Leu Ala Phe Val Ala Ala Gly
Asp Leu Ala Pro Ile Asn Ala Phe385 390 395 400Ile Gly Gly Leu Ala
Ala Gln Glu Val Met Lys Ala Cys Ser Gly Lys 405 410 415Phe Met Pro
Ile Met Gln Trp Leu Tyr Phe Asp Ala Leu Glu Cys Leu 420 425 430Pro
Glu Asp Lys Glu Ser Leu Thr Glu Asp Lys Cys Leu Pro Arg Gln 435 440
445Asn Arg Tyr Asp Gly Gln Val Ala Val Phe Gly Ser Asp Leu Gln Glu
450 455 460Lys Leu Gly Arg Gln Lys Tyr Phe Leu Val Gly Ala Gly Ala
Ile Gly465 470 475 480Cys Glu Leu Leu Lys Asn Phe Ala Met Ile Gly
Leu Gly Cys Gly Glu 485 490 495Asn Gly Glu Ile Ile Val Thr Asp Met
Asp Thr Ile Glu Lys Ser Asn 500 505 510Leu Asn Arg Gln Phe Leu Phe
Arg Pro Trp Asp Val Thr Lys Leu Lys 515 520 525Ser Asp Thr Ala Ala
Ala Ala Val His Gln Met Asn Pro His Ile Arg 530 535 540Val Thr Ser
His Gln Asn Arg Val Gly Pro Asp Thr Glu Arg Ile Tyr545 550 555
560Asp Asp Asp Phe Phe Gln Thr Leu Asp Gly Val Ala Asn Ala Leu Asp
565 570 575Asn Val Asp Ala Arg Met Tyr Met Asp Arg Arg Cys Val Tyr
Tyr Arg 580 585 590Lys Pro Leu Leu Glu Ser Gly Thr Leu Gly Thr Lys
Gly Asn Val Gln 595 600 605Val Val Ile Pro Phe Leu Thr Glu Ser Tyr
Ser Ser Ser Gln Asp Pro 610 615 620Pro Glu Lys Ser Ile Pro Ile Cys
Thr Leu Lys Asn Phe Pro Asn Ala625 630 635 640Ile Glu His Thr Leu
Gln Trp Ala Arg Asp Glu Phe Glu Gly Leu Phe 645 650 655Lys Gln Pro
Ala Glu Asn Val Asn Gln Tyr Leu Thr Asp Pro Lys Phe 660 665 670Val
Glu Arg Thr Leu Arg Leu Ala Gly Thr Gln Pro Leu Glu Val Leu 675 680
685Glu Ala Val Gln Arg Ser Leu Val Leu Gln Leu Pro Gln Ser Trp Ala
690 695 700Asp Cys Val Thr Trp Ala Cys His His Trp His Thr Gln Tyr
Ser Asn705 710 715 720Asn Ile Arg Gln Leu Leu His Asn Phe Pro Pro
Asp Gln Leu Thr Ser 725 730 735Ser Gly Ala Pro Phe Trp Ser Gly Pro
Lys Arg Cys Pro His Pro Leu 740 745 750Thr Phe Asp Val Ser Asn Pro
Leu His Leu Asp Tyr Val Met Ala Ala 755 760 765Ala Asn Leu Phe Ala
Gln Thr Tyr Gly Leu Ala Gly Ser Gln Asp Arg 770 775 780Ala Ala Val
Ala Thr Leu Leu Gln Ser Val Gln Val Pro Glu Phe Thr785 790 795
800Pro Lys Ser Gly Val Lys Ile His Val Ser Asp Gln Glu Leu Gln Ser
805 810 815Ala Asn Ala Ser Val Asp Asp Ser Arg Leu Glu Glu Leu Lys
Ala Thr 820 825 830Leu Pro Ser Pro Asp Lys Leu Pro Gly Phe Lys Met
Tyr Pro Ile Asp 835 840 845Phe Glu Lys Asp Asp Asp Ser Asn Phe His
Met Asp Phe Ile Val Ala 850 855 860Ala Ser Asn Leu Arg Ala Glu Asn
Tyr Asp Ile Pro Pro Ala Asp Arg865 870 875 880His Lys Ser Lys Leu
Ile Ala Gly Lys Ile Ile Pro Ala Ile Ala Thr 885 890 895Thr Thr Ala
Ala Val Val Gly Leu Val Cys Leu Glu Leu Tyr Lys Val 900 905 910Val
Gln Gly His Arg His Leu Asp Ser Tyr Lys Asn Gly Phe Leu Asn 915 920
925Leu Ala Leu Pro Phe Phe Gly Phe Ser Glu Pro Leu Ala Ala Pro Arg
930 935 940His Gln Tyr Tyr Asn Gln Glu Trp Thr Leu Trp Asp Arg Phe
Glu Val945 950 955 960Gln Gly Leu Gln Pro Asn Gly Glu Glu Met Thr
Leu Lys Gln Phe Leu 965 970 975Asp Tyr Phe Lys Thr Glu His Lys Leu
Glu Ile Thr Met Leu Ser Gln 980 985 990Gly Val Ser Met Leu Tyr Ser
Phe Phe Met Pro Ala Ala Lys Leu Lys 995 1000 1005Glu Arg Leu Asp
Gln Pro Met Thr Glu Ile Val Ser Arg Val Ser Lys 1010 1015 1020Arg
Lys Leu Gly Arg His Val Arg Ala Leu Val Leu Glu Leu Cys Cys1025
1030 1035 1040Asn Asp Glu Ser Gly Glu Asp Val Glu Val Pro Tyr Val
Arg Tyr Thr 1045 1050 1055Ile Arg3444DNAHomo sapiensE2 Ubc5c
3atggcgctga aacggattaa taaggaactt agtgatttgg cccgtgaccc tccagcacaa
60tgttctgcag gtccagttgg ggatgatatg tttcattggc aagccacaat tatgggacct
120aatgacagcc catatcaagg cggtgtattc tttttgacaa ttcattttcc
tacagactac 180cccttcaaac cacctaaggt tgcatttaca acaagaattt
atcatccaaa tattaacagt 240aatggcagca tttgtctcga tattctaaga
tcacagtggt cgcctgcttt aacaatttct 300aaagttcttt tatccatttg
ttcactgcta tgtgatccaa acccagatga ccccctagtg 360ccagagattg
cacggatcta taaaacagac agagataagt acaacagaat atctcgggaa
420tggactcaga agtatgccat gtga 4444147PRTHomo sapiensE2 Ubc5c 4Met
Ala Leu Lys Arg Ile Asn Lys Glu Leu Ser Asp Leu Ala Arg Asp1 5 10
15Pro Pro Ala Gln Cys Ser Ala Gly Pro Val Gly Asp Asp Met Phe His
20 25 30Trp Gln Ala Thr Ile Met Gly Pro Asn Asp Ser Pro Tyr Gln Gly
Gly 35 40 45Val Phe Phe Leu Thr Ile His Phe Pro Thr Asp Tyr Pro Phe
Lys Pro 50 55 60Pro Lys Val Ala Phe Thr Thr Arg Ile Tyr His Pro Asn
Ile Asn Ser65 70 75 80Asn Gly Ser Ile Cys Leu Asp Ile Leu Arg Ser
Gln Trp Ser Pro Ala 85 90 95Leu Thr Ile Ser Lys Val Leu Leu Ser Ile
Cys Ser Leu Leu Cys Asp 100 105 110Pro Asn Pro Asp Asp Pro Leu Val
Pro Glu Ile Ala Arg Ile Tyr Lys 115 120 125Thr Asp Arg Asp Lys Tyr
Asn Arg Ile Ser Arg Glu Trp Thr Gln Lys 130 135 140Tyr Ala
Met145584PRTHomo sapiensRING finger protein APC11 5Met Lys Val Lys
Ile Lys Cys Trp Asn Gly Val Ala Thr Trp Leu Trp1 5 10 15Val Ala Asn
Asp Glu Asn Cys Gly Ile Cys Arg Met Ala Phe Asn Gly 20 25 30Cys Cys
Pro Asp Cys Lys Val Pro Gly Asp Asp Cys Pro Leu Val Trp 35 40 45Gly
Gln Cys Ser His Cys Phe His Met His Cys Ile Leu Lys Trp Leu 50 55
60His Ala Gln Gln Val Gln Gln His Cys Pro Met Cys Arg Gln Thr Trp65
70 75 80Lys Phe Lys Glu6108PRTHomo sapiensRING finger protein ROC1
6Met Ala Ala Ala Met Asp Val Asp Thr Pro Ser Gly Thr Asn Ser Gly1 5
10 15Ala Gly Lys Lys Arg Phe Glu Val Lys Lys Trp Asn Ala Val Ala
Leu 20 25 30Trp Ala Trp Asp Ile Val Val Asp Asn Cys Ala Ile Cys Arg
Asn His 35 40 45Ile Met Asp Leu Cys Ile Glu Cys Gln Ala Asn Gln Ala
Ser Ala Thr 50 55 60Ser Glu Glu Cys Thr Val Ala Trp Gly Val Cys Asn
His Ala Phe His65 70 75 80Phe His Cys Ile Ser Arg Trp Leu Lys Thr
Arg Gln Val Cys Pro Leu 85 90 95Asp Asn Arg Glu Trp Glu Phe Gln Lys
Tyr Gly His 100 1057342DNAHomo sapiensRING finger protein ROC2
7atggccgacg tggaagacgg agaggaaacc tgcgccctgg cctctcactc cgggagctca
60ggctcaacgt cgggaggcga caagatgttc tccctcaaga agtggaaccc ggtggccatg
120tggagctggg acgtggagtg cgatacgtgc gccatctgca gggtccaggt
gatggatgcc 180tgtcttagat gtcaagctga aaacaaacaa gaggactgtg
ttgtggtctg gggagaatgt 240aatcattcct tccacaactg ctgcatgtcc
ctgtgggtga aacagaacaa tcgctgccct 300ctctgccagc aggactgggt
ggtccaaaga atcggcaaat ga 3428113PRTHomo sapiensRING finger protein
ROC2 8Met Ala Asp Val Glu Asp Gly Glu Glu Thr Cys Ala Leu Ala Ser
His1 5 10 15Ser Gly Ser Ser Gly Ser Thr Ser Gly Gly Asp Lys Met Phe
Ser Leu 20 25 30Lys Lys Trp Asn Pro Val Ala Met Trp Ser Trp Asp Val
Glu Cys Asp 35 40 45Thr Cys Ala Ile Cys Arg Val Gln Val Met Asp Ala
Cys Leu Arg Cys 50 55 60Gln Ala Glu Asn Lys Gln Glu Asp Cys Val Val
Val Trp Gly Glu Cys65 70 75 80Asn His Ser Phe His Asn Cys Cys Met
Ser Leu Trp Val Lys Gln Asn 85 90 95Asn Arg Cys Pro Leu Cys Gln Gln
Asp Trp Val Val Gln Arg Ile Gly 100 105 110Lys 92343DNAHomo
sapiensCullin CUL5 9atggcgacgt ctaatctgtt aaagaataaa ggttctcttc
agtttgaaga caaatgggat 60tttatgcgcc cgattgtttt gaagctttta cgccaggaat
ctgttacaaa acagcagtgg 120tttgatctgt tttcggatgt gcatgcagtc
tgtctttggg atgataaagg cccagcaaaa 180attcatcagg ctttaaaaga
agatattctt gagtttatta agcaggcaca ggcacgagta 240ctgagccatc
aagatgatac ggctttgcta aaagcatata ttgttgaatg gcgaaagttc
300tttacacaat gtgatatttt accaaaacct ttttgtcaac tagagattac
tttaatgggt 360aaacagggca gcaataaaaa atcaaatgtg gaagacagta
ttgttcgaaa gcttatgctt 420gatacatgga atgagtcaat cttttcaaac
ataaaaaaca gactccaaga tagtgcaatg 480aagctggtac atgctgagag
attgggagaa gcttttgatt ctcagctggt tattggagta 540agagaatcct
atgttaacct ttgttctaat cctgaggata aacttcaaat ttatagggac
600aattttgaga aggcatactt ggattcaaca gagagatttt atagaacaca
agcaccctcg 660tatttacaac caaatggtgt acagaattat atgaaatatg
cagatgctaa attaaaagaa 720gaagaaaaac gagcactacg ttatttagaa
acaagacgag aatgtaactc cgttgaagca 780ctcatggaat gctgtgtaaa
tgccctggtg acatcattta aagagactat cttagctgag 840tgccaaggca
tgatcaagag aaatgaaact gaaaaattac atttaatgtt ttcattgatg
900gacaaagttc ctaatggtat agagccaatg ttgaaagact tggaggaaca
tatcattagt 960gctggcctgg cagatatggt agcagctgct gaaactatta
ctactgactc tgagaaatac 1020gttgagcagt tacttacact atttaataga
tttagtaaac tcgtcaaaga agcttttcaa 1080gatgatccac gatttcttac
tgcaagagat aaggcgtata aagcagttgt taatgatgct 1140accatattta
aacttgaatt acctttgaag cagaaggggg tgggattaaa aactcagcct
1200gaatcaaaat gccctgagct gcttgccaat tactgtgaca tgttgctaag
aaaaacacca 1260ttaagcaaaa aactaacctc tgaagagatt gaagcaaagc
ttaaagaagt gctcttggta 1320cttaagtatg tacagaacaa agatgttttt
atgaggtatc ataaagctca tttgacacga 1380cgtcttatat tagacatctc
tgccgatagt gaaattgaag aaaacatggt agagtggcta 1440agagaagttg
gtatgccagc ggattatgta aacaagcttg ctagaatgtt tcaggacata
1500aaagtatctg aagatttgaa ccaagctttt aaggaaatgc acaaaaataa
taaattggca 1560ttaccagctg attcagttaa tataaaaatt
ctgaatgctg gcgcctggtc aagaagttct 1620gagaaagtct ttgtctcact
tcctactgaa ctggaggact tgataccgga agtagaagaa 1680ttctacaaaa
aaaatcatag tggtagaaaa ttacattggc atcatctcat gtcaaatgga
1740attataacat ttaagaatga agttggtcaa tatgatttgg aggtaaccac
gtttcagctc 1800gctgtattgt ttgcatggaa ccaaagaccc agagagaaaa
tcagctttga aaatcttaag 1860cttgcaactg aactccctga tgctgaactt
aggaggactt tatggtcttt agtagctttc 1920ccaaaactca aacggcaagt
ttttttgtat gaccctcaag tcaactcacc caaagacttt 1980acagaaggta
ccctcttctc agtgaaccag gagttcagtt taataaaaaa tgcaaaggtt
2040cagaaaaggg gtaaaatcaa cttgattgga cgtttgcagc tcactacaga
aaggatgaga 2100gaagaagaga atgaaggaat agttcaacta cgaatactaa
gaacccagga agctatcata 2160caaataatga aaatgagaaa gaaaattagt
aatgctcagc tgcagactga attagtagaa 2220attttgaaaa acatgttctt
gccacaaaag aaaatgataa aagagcaaat agagtggcta 2280atagagcaca
aatacatcag aagagatgaa tctgatatca acactttcat atatatggca 2340taa
234310861PRTHomo sapiensCullin CUL5 10Met Arg Ser Phe Ala Trp Gly
Ser Ser Gly Asp His Val Gly Asp Lys1 5 10 15Ser Glu Glu Ala Pro Gly
Ala Trp Asp Glu Val Ser Ala Val Gly Ala 20 25 30Leu Leu Gln Arg Pro
Pro His Pro Gly Ala Gly Pro Thr Gly Pro Gly 35 40 45Pro Trp Trp Glu
Leu Arg Pro Pro Val Lys Ala Trp Pro Gly Arg Glu 50 55 60Arg His Glu
Phe Ser Arg Arg Leu Val Ser Arg Glu Ser Lys Leu Lys65 70 75 80Asn
Met Ala Thr Ser Asn Leu Leu Lys Asn Lys Gly Ser Leu Gln Phe 85 90
95Glu Asp Lys Trp Asp Phe Met Arg Pro Ile Val Leu Lys Leu Leu Arg
100 105 110Gln Glu Ser Val Thr Lys Gln Gln Trp Phe Asp Leu Phe Ser
Asp Val 115 120 125His Ala Val Cys Leu Trp Asp Asp Lys Gly Pro Ala
Lys Ile His Gln 130 135 140Ala Leu Lys Glu Asp Ile Leu Glu Phe Ile
Lys Gln Ala Gln Ala Arg145 150 155 160Val Leu Ser His Gln Asp Asp
Thr Ala Leu Leu Lys Ala Tyr Ile Val 165 170 175Glu Trp Arg Lys Phe
Phe Thr Gln Cys Asp Ile Leu Pro Lys Pro Phe 180 185 190Cys Gln Leu
Glu Ile Thr Leu Met Gly Lys Gln Gly Ser Asn Lys Lys 195 200 205Ser
Asn Val Glu Asp Ser Ile Val Arg Lys Leu Met Leu Asp Thr Trp 210 215
220Asn Glu Ser Ile Phe Ser Asn Ile Lys Asn Arg Leu Gln Asp Ser
Ala225 230 235 240Met Lys Leu Val His Ala Glu Arg Leu Gly Glu Ala
Phe Asp Ser Gln 245 250 255Leu Val Ile Gly Val Arg Glu Ser Tyr Val
Asn Leu Cys Ser Asn Pro 260 265 270Glu Asp Lys Leu Gln Ile Tyr Arg
Asp Asn Phe Glu Lys Ala Tyr Leu 275 280 285Asp Ser Thr Glu Arg Phe
Tyr Arg Thr Gln Ala Pro Ser Tyr Leu Gln 290 295 300Pro Asn Gly Val
Gln Asn Tyr Met Lys Tyr Ala Asp Ala Lys Leu Lys305 310 315 320Glu
Glu Glu Lys Arg Ala Leu Arg Tyr Leu Glu Thr Arg Arg Glu Cys 325 330
335Asn Ser Val Glu Ala Leu Met Glu Cys Cys Val Asn Ala Leu Val Thr
340 345 350Ser Phe Lys Glu Thr Ile Leu Ala Glu Cys Gln Gly Met Ile
Lys Arg 355 360 365Asn Glu Thr Glu Lys Leu His Leu Met Phe Ser Leu
Met Asp Lys Val 370 375 380Pro Asn Gly Ile Glu Pro Met Leu Lys Asp
Leu Glu Glu His Ile Ile385 390 395 400Ser Ala Gly Leu Ala Asp Met
Val Ala Ala Ala Glu Thr Ile Thr Thr 405 410 415Asp Ser Glu Lys Tyr
Val Glu Gln Leu Leu Thr Leu Phe Asn Arg Phe 420 425 430Ser Lys Leu
Val Lys Glu Ala Phe Gln Asp Asp Pro Arg Phe Leu Thr 435 440 445Ala
Arg Asp Lys Ala Tyr Lys Ala Val Val Asn Asp Ala Thr Ile Phe 450 455
460Lys Leu Glu Leu Pro Leu Lys Gln Lys Gly Val Gly Leu Lys Thr
Gln465 470 475 480Pro Glu Ser Lys Cys Pro Glu Leu Leu Ala Asn Tyr
Cys Asp Met Leu 485 490 495Leu Arg Lys Thr Pro Leu Ser Lys Lys Leu
Thr Ser Glu Glu Ile Glu 500 505 510Ala Lys Leu Lys Glu Val Leu Leu
Val Leu Lys Tyr Val Gln Asn Lys 515 520 525Asp Val Phe Met Arg Tyr
His Lys Ala His Leu Thr Arg Arg Leu Ile 530 535 540Leu Asp Ile Ser
Ala Asp Ser Glu Ile Glu Glu Asn Met Val Glu Trp545 550 555 560Leu
Arg Glu Val Gly Met Pro Ala Asp Tyr Val Asn Lys Leu Ala Arg 565 570
575Met Phe Gln Asp Ile Lys Val Ser Glu Asp Leu Asn Gln Ala Phe Lys
580 585 590Glu Met His Lys Asn Asn Lys Leu Ala Leu Pro Ala Asp Ser
Val Asn 595 600 605Ile Lys Ile Leu Asn Ala Gly Ala Trp Ser Arg Ser
Ser Glu Lys Val 610 615 620Phe Val Ser Leu Pro Thr Glu Leu Glu Asp
Leu Ile Pro Glu Val Glu625 630 635 640Glu Phe Tyr Lys Lys Asn His
Ser Gly Arg Lys Leu His Trp His His 645 650 655Leu Met Ser Asn Gly
Ile Ile Thr Phe Lys Asn Glu Val Gly Gln Tyr 660 665 670Asp Leu Glu
Val Thr Thr Phe Gln Leu Ala Val Leu Phe Ala Trp Asn 675 680 685Gln
Arg Pro Arg Glu Lys Ile Ser Phe Glu Asn Leu Lys Leu Ala Thr 690 695
700Glu Leu Pro Asp Ala Glu Leu Arg Arg Thr Leu Trp Ser Leu Val
Ala705 710 715 720Phe Pro Lys Leu Lys Arg Gln Val Phe Leu Tyr Asp
Pro Gln Val Asn 725 730 735Ser Pro Lys Asp Phe Thr Glu Gly Thr Leu
Phe Ser Val Asn Gln Glu 740 745 750Phe Ser Leu Ile Lys Asn Ala Lys
Val Gln Lys Arg Gly Lys Ile Asn 755 760 765Leu Ile Gly Arg Leu Gln
Leu Thr Thr Glu Arg Met Arg Glu Glu Glu 770 775 780Asn Glu Gly Ile
Val Gln Leu Arg Ile Leu Arg Thr Gln Glu Ala Ile785 790 795 800Ile
Gln Ile Met Lys Met Arg Lys Lys Ile Ser Asn Ala Gln Leu Gln 805 810
815Thr Glu Leu Val Glu Ile Leu Lys Asn Met Phe Leu Pro Gln Lys Lys
820 825 830Met Ile Lys Glu Gln Ile Glu Trp Leu Ile Glu His Lys Tyr
Ile Arg 835 840 845Arg Asp Glu Ser Asp Ile Asn Thr Phe Ile Tyr Met
Ala 850 855 860112469DNAHomo sapiensCullin APC2 11atggcggcgg
cagttgtggt ggcggagggg gacagcgact cccggcccgg acaggagttg 60ttagtggcct
ggaacaccgt gagcaccggc ctggtgccgc cggctgcgct ggggctggtg
120tcttcccgga ccagcggtgc agtcccgcca aaggaagagg agctccgggc
ggcggtggag 180gttctgaggg gccacgggct acactcggtc ctggaggagt
ggttcgtgga ggtgctgcag 240aacgatctgc aggccaacat ctcccctgag
ttctggaatg ccatctccca atgcgagaac 300tctgcggatg agccccagtg
ccttttgcta ctccttgacg cttttggcct gctggagagc 360cgcctggatc
cctacctgcg tagcctagag ctgctggaga aatggactcg cctgggcttg
420ctgatgggca ctggtgctca ggggctgcga gaagaagtcc acactatgtt
gcgcggagtc 480ttgttcttta gcacccccag aaccttccaa gagatgatcc
agcgtctgta tgggtgcttc 540ttgagagtct atatgcagag taagaggaag
ggggaagggg gcacagaccc ggaactggaa 600ggggagctgg acagccggta
tgcccgtcgc cggtactacc ggctcctgca gagcccgctg 660tgtgcagggt
gcagcagtga caagcaacag tgctggtgtc gccaggctct ggagcagttc
720catcagctca gccaggtctt acacaggctc agtctgctgg agcgggtcag
tgccgaggct 780gtgaccacca ccctgcacca ggtgacccgg gagaggatgg
aggaccgttg ccggggcgag 840tacgagcgct ccttcctgcg tgagttccac
aagtggatcg agcgggtggt cggctggctc 900ggcaaggtgt tcctgcagga
cggccccgcc aggcccgcat ctcccgaggc cggcaacacc 960ctgcgccgct
ggcgctgcca cgtgcaaagg ttcttctacc gcatctacgc cagcctgcgc
1020atcgaggagc tcttcagcat cgtccgagac ttcccagact cccggccagc
catcgaggac 1080ctcaagtact gcctggagag gacggaccag aggcagcagc
tgctcgtgtc cctcaaggct 1140gccctggaga ctcggctcct gcatccaggc
gtcaacacgt gtgacatcat caccctctat 1200atctctgcca tcaaggcgct
gcgcgtgctg gacccttcca tggtcatcct ggaggtggcc 1260tgtgagccta
tccgccgcta cctgaggacg cgggaggaca cagtgcggca gattgtggct
1320gggctgacgg gggactcgga cgggacaggg gacctggctg ttgagctgtc
caagaccgac 1380ccggcgagcc tggagacagg ccaggacagt gaggatgact
caggcgagcc agaggactgg 1440gtcccggacc ctgtggatgc cgatccaggg
aagtcgagct ccaagcggcg ttcatcggac 1500atcatcagcc tgctggtcag
catctacggc agcaaggacc tcttcatcaa tgagtaccgc 1560tcgctgctgg
ccgaccgcct gctgcaccag ttcagcttca gccccgagcg ggagatccgc
1620aacgtggagc tgctgaagct gcgctttggc gaggccccaa tgcacttctg
tgaagtcatg 1680ctgaaggaca tggcggactc ccgccgcatc aatgccaaca
tccgggagga ggatgagaag 1740cggccagcag aggagcagcc accgttcggg
gtctacgctg tcatcctgtc cagtgagttc 1800tggccgccct tcaaggacga
gaagctggag gtccccgagg atatcagggc agccctggag 1860gcttactgca
agaagtatga gcagctcaag gccatgcgga ccctcagttg gaagcacacc
1920ctgggcctgg tgaccatgga cgtggagctg gccgaccgca cgctgtctgt
ggcggtcacc 1980ccagtacagg cggtgatctt gctgtatttt caggaccaag
ccagctggac cctggaggaa 2040ctgagcaagg cggtgaaaat gcccgtggcg
ctgctgcggc ggcggatgtc cgtgtggctg 2100cagcagggtg tgctgcgtga
ggagcccccc ggcaccttct ctgtcattga ggaggagcgg 2160cctcaggacc
gggacaacat ggtgctcatt gacagtgacg acgagagcga ctccggcatg
2220gcctcccagg ccgaccagaa ggaggaggag ctgctgctct tctggacgta
catccaggcc 2280atgctgacca acctggagag cctctcactg gatcgtatct
acaacatgct ccgcatgttt 2340gtggtgactg ggcctgcact ggccgagatt
gacctgcagg agctgcaggg ctacctgcag 2400aagaaggtgc gggaccagca
gctcgtctac tcggccggcg tctaccgcct gcccaagaac 2460tgcagctga
246912822PRTHomo sapiensCullin APC2 12Met Ala Ala Ala Val Val Val
Ala Glu Gly Asp Ser Asp Ser Arg Pro1 5 10 15Gly Gln Glu Leu Leu Val
Ala Trp Asn Thr Val Ser Thr Gly Leu Val 20 25 30Pro Pro Ala Ala Leu
Gly Leu Val Ser Ser Arg Thr Ser Gly Ala Val 35 40 45Pro Pro Lys Glu
Glu Glu Leu Arg Ala Ala Val Glu Val Leu Arg Gly 50 55 60His Gly Leu
His Ser Val Leu Glu Glu Trp Phe Val Glu Val Leu Gln65 70 75 80Asn
Asp Leu Gln Ala Asn Ile Ser Pro Glu Phe Trp Asn Ala Ile Ser 85 90
95Gln Cys Glu Asn Ser Ala Asp Glu Pro Gln Cys Leu Leu Leu Leu Leu
100 105 110Asp Ala Phe Gly Leu Leu Glu Ser Arg Leu Asp Pro Tyr Leu
Arg Ser 115 120 125Leu Glu Leu Leu Glu Lys Trp Thr Arg Leu Gly Leu
Leu Met Gly Thr 130 135 140Gly Ala Gln Gly Leu Arg Glu Glu Val His
Thr Met Leu Arg Gly Val145 150 155 160Leu Phe Phe Ser Thr Pro Arg
Thr Phe Gln Glu Met Ile Gln Arg Leu 165 170 175Tyr Gly Cys Phe Leu
Arg Val Tyr Met Gln Ser Lys Arg Lys Gly Glu 180 185 190Gly Gly Thr
Asp Pro Glu Leu Glu Gly Glu Leu Asp Ser Arg Tyr Ala 195 200 205Arg
Arg Arg Tyr Tyr Arg Leu Leu Gln Ser Pro Leu Cys Ala Gly Cys 210 215
220Ser Ser Asp Lys Gln Gln Cys Trp Cys Arg Gln Ala Leu Glu Gln
Phe225 230 235 240His Gln Leu Ser Gln Val Leu His Arg Leu Ser Leu
Leu Glu Arg Val 245 250 255Ser Ala Glu Ala Val Thr Thr Thr Leu His
Gln Val Thr Arg Glu Arg 260 265 270Met Glu Asp Arg Cys Arg Gly Glu
Tyr Glu Arg Ser Phe Leu Arg Glu 275 280 285Phe His Lys Trp Ile Glu
Arg Val Val Gly Trp Leu Gly Lys Val Phe 290 295 300Leu Gln Asp Gly
Pro Ala Arg Pro Ala Ser Pro Glu Ala Gly Asn Thr305 310 315 320Leu
Arg Arg Trp Arg Cys His Val Gln Arg Phe Phe Tyr Arg Ile Tyr 325 330
335Ala Ser Leu Arg Ile Glu Glu Leu Phe Ser Ile Val Arg Asp Phe Pro
340 345 350Asp Ser Arg Pro Ala Ile Glu Asp Leu Lys Tyr Cys Leu Glu
Arg Thr 355 360 365Asp Gln Arg Gln Gln Leu Leu Val Ser Leu Lys Ala
Ala Leu Glu Thr 370 375 380Arg Leu Leu His Pro Gly Val Asn Thr Cys
Asp Ile Ile Thr Leu Tyr385 390 395 400Ile Ser Ala Ile Lys Ala Leu
Arg Val Leu Asp Pro Ser Met Val Ile 405 410 415Leu Glu Val Ala Cys
Glu Pro Ile Arg Arg Tyr Leu Arg Thr Arg Glu 420 425 430Asp Thr Val
Arg Gln Ile Val Ala Gly Leu Thr Gly Asp Ser Asp Gly 435 440 445Thr
Gly Asp Leu Ala Val Glu Leu Ser Lys Thr Asp Pro Ala Ser Leu 450 455
460Glu Thr Gly Gln Asp Ser Glu Asp Asp Ser Gly Glu Pro Glu Asp
Trp465 470 475 480Val Pro Asp Pro Val Asp Ala Asp Pro Gly Lys Ser
Ser Ser Lys Arg 485 490 495Arg Ser Ser Asp Ile Ile Ser Leu Leu Val
Ser Ile Tyr Gly Ser Lys 500 505 510Asp Leu Phe Ile Asn Glu Tyr Arg
Ser Leu Leu Ala Asp Arg Leu Leu 515 520 525His Gln Phe Ser Phe Ser
Pro Glu Arg Glu Ile Arg Asn Val Glu Leu 530 535 540Leu Lys Leu Arg
Phe Gly Glu Ala Pro Met His Phe Cys Glu Val Met545 550 555 560Leu
Lys Asp Met Ala Asp Ser Arg Arg Ile Asn Ala Asn Ile Arg Glu 565 570
575Glu Asp Glu Lys Arg Pro Ala Glu Glu Gln Pro Pro Phe Gly Val Tyr
580 585 590Ala Val Ile Leu Ser Ser Glu Phe Trp Pro Pro Phe Lys Asp
Glu Lys 595 600 605Leu Glu Val Pro Glu Asp Ile Arg Ala Ala Leu Glu
Ala Tyr Cys Lys 610 615 620Lys Tyr Glu Gln Leu Lys Ala Met Arg Thr
Leu Ser Trp Lys His Thr625 630 635 640Leu Gly Leu Val Thr Met Asp
Val Glu Leu Ala Asp Arg Thr Leu Ser 645 650 655Val Ala Val Thr Pro
Val Gln Ala Val Ile Leu Leu Tyr Phe Gln Asp 660 665 670Gln Ala Ser
Trp Thr Leu Glu Glu Leu Ser Lys Ala Val Lys Met Pro 675 680 685Val
Ala Leu Leu Arg Arg Arg Met Ser Val Trp Leu Gln Gln Gly Val 690 695
700Leu Arg Glu Glu Pro Pro Gly Thr Phe Ser Val Ile Glu Glu Glu
Arg705 710 715 720Pro Gln Asp Arg Asp Asn Met Val Leu Ile Asp Ser
Asp Asp Glu Ser 725 730 735Asp Ser Gly Met Ala Ser Gln Ala Asp Gln
Lys Glu Glu Glu Leu Leu 740 745 750Leu Phe Trp Thr Tyr Ile Gln Ala
Met Leu Thr Asn Leu Glu Ser Leu 755 760 765Ser Leu Asp Arg Ile Tyr
Asn Met Leu Arg Met Phe Val Val Thr Gly 770 775 780Pro Ala Leu Ala
Glu Ile Asp Leu Gln Glu Leu Gln Gly Tyr Leu Gln785 790 795 800Lys
Lys Val Arg Asp Gln Gln Leu Val Tyr Ser Ala Gly Val Tyr Arg 805 810
815Leu Pro Lys Asn Cys Ser 8201376PRTHomo sapienshuman ubiquitin
13Met Gln Ile Phe Val Lys Thr Leu Thr Gly Lys Thr Ile Thr Leu Glu1
5 10 15Val Glu Pro Ser Asp Thr Ile Glu Asn Val Lys Ala Lys Ile Gln
Asp 20 25 30Lys Glu Gly Ile Pro Pro Asp Gln Gln Arg Leu Ile Phe Ala
Gly Lys 35 40 45Gln Leu Glu Asp Gly Arg Thr Leu Ser Asp Tyr Asn Ile
Gln Lys Glu 50 55 60Ser Thr Leu His Leu Val Leu Arg Leu Arg Gly
Gly65 70 751484PRTArtificial SequenceDescription of Artificial
SequenceFLAG- ubiquitin 14Met Asp Tyr Lys Asp Asp Asp Asp Lys Gln
Ile Phe Val Lys Thr Leu1 5 10 15Thr Gly Lys Thr Ile Thr Leu Glu Val
Glu Pro Ser Asp Thr Ile Glu 20 25 30Asn Val Lys Ala Lys Ile Gln Asp
Lys Glu Gly Ile Pro Pro Asp Gln 35 40 45Gln Arg Leu Ile Phe Ala Gly
Lys Gln Leu Glu Asp Gly Arg Thr Leu 50 55 60Ser Asp Tyr Asn Ile Gln
Lys Glu Ser Thr Leu His Leu Val Leu Arg65 70 75 80Leu Arg Gly
Gly1585PRTArtificial SequenceDescription of Artificial
SequenceFLAG-Cys-ubiquitin 15Met Asp Tyr Lys Asp Asp Asp Asp Lys
Cys Gln Ile Phe Val Lys Thr1 5 10 15Leu Thr Gly Lys Thr Ile Thr Leu
Glu Val Glu Pro Ser Asp Thr Ile 20 25 30Glu Asn Val Lys Ala Lys Ile
Gln Asp Lys Glu Gly Ile Pro Pro Asp 35 40
45Gln Gln Arg Leu Ile Phe Ala Gly Lys Gln Leu Glu Asp Gly Arg Thr
50 55 60Leu Ser Asp Tyr Asn Ile Gln Lys Glu Ser Thr Leu His Leu Val
Leu65 70 75 80Arg Leu Arg Gly Gly 85168PRTArtificial
SequenceDescription of Artificial SequenceFLAG peptide tag 16Asp
Tyr Lys Asp Asp Asp Asp Lys1 5179PRTArtificial SequenceDescription
of Artificial SequenceFLAG-Cys 17Asp Tyr Lys Asp Asp Asp Asp Lys
Cys1 51886PRTArtificial SequenceDescription of Artificial
SequenceFLAG-Ala-Cys-ubiquitin 18Met Asp Tyr Lys Asp Asp Asp Asp
Lys Ala Cys Gln Ile Phe Val Lys1 5 10 15Thr Leu Thr Gly Lys Thr Ile
Thr Leu Glu Val Glu Pro Ser Asp Thr 20 25 30Ile Glu Asn Val Lys Ala
Lys Ile Gln Asp Lys Glu Gly Ile Pro Pro 35 40 45Asp Gln Gln Arg Leu
Ile Phe Ala Gly Lys Gln Leu Glu Asp Gly Arg 50 55 60Thr Leu Ser Asp
Tyr Asn Ile Gln Lys Glu Ser Thr Leu His Leu Val65 70 75 80Leu Arg
Leu Arg Gly Gly 851942DNAArtificial SequenceDescription of
Artificial SequenceFLAG-Cys-ubiquitin site-directed mutagenesis
primer 19ccccccaagc tttgcatgca gattttcgtg aagaccctga cc
422045DNAArtificial SequenceDescription of Artificial
SequenceFLAG-Ala-Cys-ubiquitin site-directed mutagenesis primer
20ccccccaagc ttgcgtgcat gcagattttc gtgaagaccc tgacc
45216PRTArtificial SequenceDescription of Artificial
SequenceN-terminal His6-tag 21His His His His His His1 5
* * * * *
References