U.S. patent application number 15/406541 was filed with the patent office on 2017-12-28 for high-sensitive fluorescent energy transfer assay using fluorescent amino acids and fluorescent proteins.
The applicant listed for this patent is The Regents of the University of California. Invention is credited to Jiayu LIAO, Yan LIU, Yang SONG, Yongfeng ZHAO.
Application Number | 20170370916 15/406541 |
Document ID | / |
Family ID | 41091568 |
Filed Date | 2017-12-28 |
United States Patent
Application |
20170370916 |
Kind Code |
A1 |
LIAO; Jiayu ; et
al. |
December 28, 2017 |
HIGH-SENSITIVE FLUORESCENT ENERGY TRANSFER ASSAY USING FLUORESCENT
AMINO ACIDS AND FLUORESCENT PROTEINS
Abstract
The disclosure provides method and composition utilizing
fluorescent amino acids and fluorescent proteins comprising a
moiety capable of undergoing FRET. The methods and compositions of
the disclosure are useful in analyzing protein structure and
function, and screening molecular inhibitors.
Inventors: |
LIAO; Jiayu; (Carlsbad,
CA) ; SONG; Yang; (Riverside, CA) ; ZHAO;
Yongfeng; (Riverside, CA) ; LIU; Yan;
(Riverside, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Regents of the University of California |
Oakland |
CA |
US |
|
|
Family ID: |
41091568 |
Appl. No.: |
15/406541 |
Filed: |
January 13, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14604698 |
Jan 24, 2015 |
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15406541 |
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12933780 |
Jan 18, 2011 |
8940506 |
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PCT/US2009/037907 |
Mar 21, 2009 |
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14604698 |
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61038526 |
Mar 21, 2008 |
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61098722 |
Sep 19, 2008 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 14/00 20130101;
C07K 14/001 20130101; G01N 33/542 20130101; C07K 7/06 20130101 |
International
Class: |
G01N 33/542 20060101
G01N033/542; C07K 7/06 20060101 C07K007/06; C07K 14/00 20060101
C07K014/00 |
Claims
1-24. (canceled)
25. A method of performing Forster resonance energy transfer
(FRET)-based high throughput screening (HTS), the method
comprising: a) providing a sample in a plurality of wells of a
multi-well plate, wherein the sample comprises a first polypeptide
comprising a CyPet moiety and a second polypeptide comprising a
YPet moiety; b) contacting the sample with a library of candidate
agents; c) exposing the plurality of wells to a first wavelength of
light, wherein the first wavelength of light is suitable for
exciting the CyPet moiety; d) measuring a second wavelength of
light in the plurality of wells, wherein the second wavelength of
light is emitted from the YPet moiety; and e) calculating the
ratiometric FRET signal between the CyPet moiety and the YPet
moiety in each of the plurality of wells.
26. The method of claim 25, further comprising f) comparing the
ratiometric FRET signal calculated in step e) to a standard.
27. The method of claim 25, further comprising f) comparing the
ratiometric FRET signal calculated in step e) to a control
ratiometric FRET signal obtained by a method comprising: i)
providing a second sample in one or more wells of a multi-well
plate, wherein the second sample comprises the first polypeptide
comprising the CyPet moiety and the second polypeptide comprising
the YPet moiety; ii) exposing the one or more wells to a first
wavelength of light, wherein the first wavelength of light is
suitable for exciting the CyPet moiety; iii) measuring a second
wavelength of light in the one or more wells, wherein the second
wavelength of light is emitted from the YPet moiety; and iv)
calculating the control ratiometric FRET signal between the CyPet
moiety and the YPet moiety in the one or more wells.
28. The method of claim 25, wherein the first wavelength of light
is about 414 nm.
29. The method of claim 25, wherein the second wavelength of light
is about 530 nm.
30. The method of claim 25, wherein the first polypeptide further
comprises a SUMO1 polypeptide.
31. The method of claim 30, wherein the SUMO1 polypeptide is fused
to the CyPet moiety.
32. The method of claim 25, wherein the second polypeptide further
comprises an additional polypeptide selected from the group
consisting of a SUMO ligase, a SUMO-conjugating enzyme, and a
SUMO-specific peptidase.
33. The method of claim 32, wherein the additional polypeptide is
fused to the YPet moiety.
34. The method of claim 25, wherein at least one of the candidate
agents in the library decreases the ratiometric FRET signal between
the first and second polypeptides.
35. The method of claim 25, wherein the multi-well plate is a
96-well plate or 384-well plate.
36. The method of claim 25, wherein the sample comprises a
mammalian cell expressing the first polypeptide and the second
polypeptide.
37. The method of claim 25, wherein at least one of the candidate
agents in the library is an inhibitor.
38. The method of claim 37, wherein the at least one candidate
agent disrupts the interaction between the first and second
polypeptides.
39. The method of claim 25, wherein the library of candidate agents
is a small molecule library.
40. The method of claim 25, wherein the library of candidate agents
is selected from the group consisting of a library of drugs, a
chemical library, and a library of biologics.
41. A kit comprising: a) a multi-well plate; b) a first polypeptide
comprising a CyPet moiety; and c) a second polypeptide comprising a
YPet moiety and a polypeptide selected from the group consisting of
a SUMO ligase, a SUMO-conjugating enzyme, and a SUMO-specific
peptidase.
42. The kit of claim 41, further comprising d) one or more
candidate agents selected from the group consisting of a drug, a
chemical, and a biologic.
43. The kit of claim 41, wherein the first polypeptide further
comprises a SUMO1 polypeptide.
44. The kit of claim 41, wherein the multi-well plate is a 96-well
plate or 384-well plate.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 12/933,780, filed Jan. 18, 2011, which is a U.S. National Stage
Application filed under 35 U.S.C. .sctn.371 and claims priority to
International Application No. PCT/US2009/037907, filed on Mar. 21,
2009, which application claims priority under 35 U.S.C. .sctn.119
to U.S. Provisional Application No. 61/038,526, filed Mar. 21,
2008, and U.S. Provisional Application No. 61/098,722, filed Sep.
19, 2008, the disclosures of which are incorporated herein by
reference.
FIELD OF THE INVENTION
[0002] The disclosure relates to the field of protein biochemistry
and protein analysis. More particularly, the disclosure relates to
the field of compositions and methods for producing proteins that
include fluorescent amino acids or fluorescent proteins and using
such fluorescent amino acids or fluorescent proteins in FRET
analyses or protein-protein or amino acid-amino acid, or amino
acid-protein interactions, or high-throughput screenings.
BACKGROUND
[0003] Proteins carry out virtually all of the complex processes of
life. Accordingly, understanding their structure, function and
interactions with the environment provide information useful in the
development of diagnostic, prognostics, therapies and the like.
SUMMARY
[0004] The disclosure provides peptides, polypeptides, proteins, or
any other composition comprising at least two fluorescent amino
acids or two fluorophores that are capable of undergoing FRET,
wherein one of the amino acids comprises a fluorophore and one
comprises a quencher of the FRET signal when placed in close
proximity to the fluorophore. In one embodiment, the peptide,
polypeptide protein or composition comprises a first fluorescent
amino acid comprising a quencher amino acid having a general
structure I:
##STR00001##
wherein n is any integer between 1 and 10 inclusive (e.g., 1, 2, 3,
4, 5 etc.) and R.sub.1 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo.
[0005] In yet a further embodiment, the composition further
contains a fluorophore amino acid having a general structure
II:
##STR00002##
wherein n is any integer between 1 and 10 inclusive (e.g., 1, 2, 3,
4, 5 etc.) and R.sub.1 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.1 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring; R.sub.2 is selected from the
group consisting of: H, aryl, substituted aryl, alkyl, substituted
alkyl, carboxyl, aminocarbonyl, alkylsulfonylaminocarboxyl,
alkoxycarbonyl, and halo, or R.sub.2 and R.sub.1, together with the
carbons to which they are bound, can be joined to form a 4 to 7
membered ring or a substituted 4 to 7 membered ring, or R.sub.2 and
R.sub.3, together with the carbons to which they are bound, can be
joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring; R.sub.3 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.3 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring, or R.sub.3 and R.sub.4, together
with the carbons to which they are bound, can be joined to form a 4
to 7 membered ring or a substituted 4 to 7 membered ring; R.sub.4
is selected from the group consisting of: H, aryl, substituted
aryl, alkyl, substituted alkyl, carboxyl, aminocarbonyl,
alkylsulfonylaminocarboxyl, alkoxycarbonyl, and halo, or R.sub.4
and R.sub.3, together with the carbons to which they are bound, can
be joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring. In yet another embodiment, the fluorescent amino
acid comprises a general structure III:
##STR00003##
wherein R.sub.1 is selected from the group consisting of: H, aryl,
substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.1 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring; R.sub.2 is selected from the
group consisting of: H, aryl, substituted aryl, alkyl, substituted
alkyl, carboxyl, aminocarbonyl, alkylsulfonylaminocarboxyl,
alkoxycarbonyl, and halo, or R.sub.2 and R.sub.1, together with the
carbons to which they are bound, can be joined to form a 4 to 7
membered ring or a substituted 4 to 7 membered ring, or R.sub.2 and
R.sub.3, together with the carbons to which they are bound, can be
joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring; R.sub.3 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.3 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring, or R.sub.3 and R.sub.4, together
with the carbons to which they are bound, can be joined to form a 4
to 7 membered ring or a substituted 4 to 7 membered ring; R.sub.4
is selected from the group consisting of: H, aryl, substituted
aryl, alkyl, substituted alkyl, carboxyl, aminocarbonyl,
alkylsulfonylaminocarboxyl, alkoxycarbonyl, and halo, or R.sub.4
and R.sub.3, together with the carbons to which they are bound, can
be joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring. In a specific embodiment, the fluorescent amino acid
comprises a coumarin fluorescent amino acid comprising the
structure IV:
##STR00004##
and a quenching NBD fluorescent amino acid comprising the general
structure V:
##STR00005##
In yet another embodiment, the composition comprises a sequence
containing a structure selected from I or V within about 1-15
(e.g., 1-10 nm, 2-8 nm etc.) of a fluorescent amino acid selected
from the group consisting of II, III, or IV. In yet another
embodiment, the fluorescent amino acid and quencher amino acid are
spaced about 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids from each
other.
[0006] The disclosure provides a method of identifying a binding
ligand or substrate for a target polypeptide comprising: providing
a polynucleotide comprising at least one codon that results in the
incorporation of at least one chromophore or fluorescent amino acid
upon translation, wherein the chromophore or fluorescent amino acid
comprises a first acceptor or donor chromophore or fluorophore
moiety; translating the polynucleotide to obtain a labeled
polypeptide comprising the at least one chromophore or fluorescent
amino acid; contacting labeled polypeptide with a putative binding
ligand comprising a second acceptor or donor chromophore or
fluorophore moiety, wherein the first and second acceptor or donor
chromophore or fluorophore moieties are different, wherein the
first and second acceptor or donor chromophore or fluorophore
moieties are selected to undergo Forster resonance energy transfer
(FRET) when a binding ligand is bound to a target polypeptide, and
identifying FRET, wherein the presence of FRET is indicative that
the putative binding ligand binds to the target polypeptide thereby
identifying the binding ligand. In one embodiment, the method is
carried out in a cell-free system. In another embodiment, the
method is carried out in a cell. In yet another embodiment, the
acceptor is a quenching moiety. In yet a further embodiment, a
first polypeptide comprises a fluorescent amino acid having the
general structure II, II, or IV and second polypeptide comprises a
fluorescent amino acid having the general structure I or V.
[0007] The disclosure also provides a method of identifying a
structure of a polypeptide comprising: providing a polynucleotide
comprising at least two codons that results in the incorporation of
at least two chromophore or fluorescent amino acid upon
translation, wherein the chromophore or fluorescent amino acid;
translating the polynucleotide to obtain a labeled polypeptide
comprising the at least two chromophore or fluorescent amino acid
comprising at least a first and second chromophore or fluorophore
moieties, wherein the first and second acceptor or donor
chromophore or fluorophore moieties are different, wherein the
first and second acceptor or donor chromophore or fluorophore
moieties are selected to undergo Forster resonance energy transfer
(FRET), and identifying FRET, wherein the presence of FRET is
indicative that the at least two amino acids are within a selected
distance from one another, thereby providing a structure of the
polypeptide. In one embodiment, the method is carried out in a
cell-free system. In another embodiment, the method is carried out
in a cell. In yet another embodiment, the acceptor is a quenching
moiety.
[0008] The fluorophore pairs of the disclosure can be used in
combination with nucleic acids, lipids and other biological
molecules in addition to proteins and polypeptide. Furthermore, the
fluorophore pairs can be used in combination with solid substrates
(e.g., tissue culture plate, beads, slides, nanoparticles and the
like).
[0009] The disclosure also provide a method of identify
protein-protein interactions in living cells.
[0010] The disclosure also provides a method of identifying
molecules that inhibit the cleavage of peptide flanking by the
fluorescent amino acids.
[0011] The disclosure also provides a method of identifying
molecules that disrupt the protein-protein interaction in living
cells.
[0012] The disclosure also provide the use of an NBD or NBD
derivative and coumarin or coumarin derivative as fluorophores
bound to substrates including bead, solid surface and biological
compounds including nucleic acids, lipids and the like.
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] FIG. 1 depicts an exemplary methodology of the
disclosure.
[0014] FIG. 2 depicts a process of incorporating fluorescent amino
acids into a polypeptide.
[0015] FIG. 3A-B depicts the structures of fluorescent amino acids
and derivatives. (B) Structures of NBD (left) and CUM (right)
fluorescent amino acids.
[0016] FIG. 4 shows the SUMO pathway and the SUMOylation in the
JAK/STAT pathway.
[0017] FIG. 5 shows process of development of orthogonal pair of
aminoacyl-tRNA synthetase (aaRS) and amber suppressor tRNA to
incorporate the fluorescent amino acid L-(7-hydroxycoumarin-4-yl)
ethylglycine.
[0018] FIG. 6 depicts a concept of the disclosure. Although the
SUMO pathway is depicted, any polypeptide interaction can be
substituted.
[0019] FIG. 7 shows a development of an orthogonal pair of aaRS and
opal/ochre suppressor tRNA to incorporate
3-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-L-alanine (NBD-alanine)
into proteins in mammalian cells and test the FRET efficiency of
two fluorescent amino acids in the FRET reporter.
[0020] FIG. 8 shows a scheme of EcTyrRS selection in yeast.
[0021] FIG. 9 shows the structure of a tRNA.sup.tyr (SEQ ID
NO:1).
[0022] FIG. 10 shows Active site of E. coli tyrosyl-tRNA
synthetase.
[0023] FIG. 11 shows a method of testing incorporation efficiency
and specificity in mammalian cells.
[0024] FIG. 12 shows a selection process for incorporation of
fluorescent amino acids.
[0025] FIG. 13 shows the fluorescent intensity of peptide I
solution with different concentration excited at 340 nm.
[0026] FIG. 14 shows fluorescent intensity of peptide I (6AA
between coumarin and NBD) and II (4AA between coumarin and NBD)
solution with different concentration (a: 200 .mu.M; b: 100 .mu.M)
excited at 340 nm.
[0027] FIG. 15 shows fluorescent intensity of peptide I solution
and interaction with SENP2 excited at 340 nm.
[0028] FIG. 16 shows fluorescent intensity of peptide I solution
and interaction with SENP2 excited at 340 nm at different time
point, checking at emission wavelength at 555 nm.
[0029] FIG. 17 depicts conjugation and deconjugation of SUMO to and
from substrate proteins require multiples enzymes.
DETAILED DESCRIPTION
[0030] As used herein and in the appended claims, the singular
forms "a," "and," and "the" include plural referents unless the
context clearly dictates otherwise. Thus, for example, reference to
"an fluorescent amino acid" includes a plurality of such
fluorescent amino acids and reference to "the protein" includes
reference to one or more proteins, and so forth.
[0031] Also, the use of "or" means "and/or" unless stated
otherwise. Similarly, "comprise," "comprises," "comprising"
"include," "includes," and "including" are interchangeable and not
intended to be limiting.
[0032] It is to be further understood that where descriptions of
various embodiments use the term "comprising," those skilled in the
art would understand that in some specific instances, an embodiment
can be alternatively described using language "consisting
essentially of" or "consisting of."
[0033] Although methods and materials similar or equivalent to
those described herein can be used in the practice of the disclosed
methods and compositions, the exemplary methods, devices and
materials are described herein.
[0034] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood to one of
ordinary skill in the art to which this disclosure belongs. Thus,
as used throughout the instant application, the following terms
shall have the following meanings.
[0035] The phenomenon that Forster resonance energy transfer (FRET)
occurs between a fluorophore and either (i) a second fluorophore
with and overlapping emission-excitation spectrum or (ii) a
quenching moiety that absorbs at the emission spectrum of the first
fluorophore is useful for studying biological conditions. Such
techniques have been used extensively in biological research to
study protein conformational changes, protein interactions,
intracellular signaling pathways, and discover novel biological
bioactive chemicals for drug development. Typically, one
fluorophore serves as an emitter and the second fluorophore serves
as a quencher. During typical FRET assays one of the fluorophores
is excited by an external excitation wavelength to induce
fluorescence, the emitted spectrum from the first fluorophore will
be absorbed by the second, quenching, fluorophore provide a
distinct excitation emission spectrum. Where a change in the
distance between the two fluorophores occurs, the excitation of the
second fluorophore is modulated and thus provides a second
distinctive excitation emission spectrum. This change in
excitation-emission spectrums during a FRET assay is indicative of
a biological effect, event or structure. However, in these systems
the bulky size of traditional fluorophores used in FRET-based
assays, e.g., the green fluorescent protein (GFP) variants, result
in spatial hindrance and interference.
[0036] The disclosure uses fluorescent amino acid with side chain
groups which can be genetically encoded and incorporated into
peptides, polypeptide or proteins with high specificity to measure
protein function and structure. Alternatively, and as described
more thoroughly elsewhere herein, the amino acids may be
incorporated into a desired peptide or polypeptide using standard
peptide synthesis techniques.
[0037] The use of fluorescent amino acids has been described,
however, proper quencher and emitter FRET pairs have not been
identified. The use of a FRET pair of fluorescent amino acid
provides the ability to measure biological and physical properties
of peptide, polypeptide and proteins. Using the FRET pairs
described herein a FRET reporter molecule with fluorescent amino
acids can be used to facilitate the high-throughput screening of,
for example, SUMO ligase and protease inhibitors or activity, which
will be important in studies of cytokine signaling pathways,
protein folding, protease activity and ligand binding pairs. The
utilization of fluorescent amino acids in FRET-based
high-throughput screening is a novel method to prevent the
drawbacks of GFP variants, and it will broaden the application of
fluorescent amino acids in biological research.
[0038] An "amino acid" is a molecule having the structure wherein a
central carbon atom (the -carbon atom) is linked to a hydrogen
atom, a carboxylic acid group (the carbon atom of which is referred
to herein as a "carboxyl carbon atom"), an amino group (the
nitrogen atom of which is referred to herein as an "amino nitrogen
atom"), and a side chain group, R. When incorporated into a
peptide, polypeptide, or protein, an amino acid loses one or more
atoms of its amino acid carboxylic groups in the dehydration
reaction that links one amino acid to another. As a result, when
incorporated into a protein, an amino acid is referred to as an
"amino acid residue."
[0039] An fluorescent amino acid comprises a structure wherein a
central carbon atom is linked to a hydrogen atom, a carboxylic acid
group (the carbon atom of which is referred to herein as a
"carboxyl carbon atom"), an amino group (the nitrogen atom of which
is referred to herein as an "amino nitrogen atom"), and a side
chain group, R, wherein the R group is any substituent other than
one used in the twenty natural amino acids. See, e.g., Biochemistry
by L. Stryer, 3rd ed. 1988, Freeman and Company, New York, for
structures of the twenty natural amino acids. Because the
fluorescent amino acids typically differ from the natural amino
acids in side chain only, the fluorescent amino acids form amide
bonds with other amino acids, e.g., natural or unnatural, in the
same manner in which they are formed in naturally occurring
proteins. However, the fluorescent amino acids have side chain
groups that distinguish them from the natural amino acids.
[0040] A fluorescent amino acid refers to a chemical compound
comprising the general structure of an amino acid comprising,
however, a non-naturally occurring chemical group(s). Examples of
fluorescent amino acids include, but are not limited to, an
fluorescent analogue of a tyrosine amino acid; an fluorescent
analogue of a glutamine amino acid; an fluorescent analogue of a
phenylalanine amino acid; an fluorescent analogue of a serine amino
acid; an fluorescent analogue of a threonine amino acid; an alkyl,
aryl, acyl, azido, cyano, halo, hydrazine, hydrazide, hydroxyl,
alkenyl, alkynl, ether, thiol, sulfonyl, seleno, ester, thioacid,
borate, boronate, phospho, phosphono, phosphine, heterocyclic,
enone, imine, aldehyde, hydroxylamine, keto, or amino substituted
amino acid, or any combination thereof; an amino acid with a
photoactivatable cross-linker; a spin-labeled amino acid; a
fluorescent amino acid; an amino acid with a novel functional
group; an amino acid that covalently or noncovalently interacts
with another molecule; a metal binding amino acid; a
metal-containing amino acid; a radioactive amino acid; a photocaged
and/or photoisomerizable amino acid; a biotin or biotin-analogue
containing amino acid; a glycosylated or carbohydrate modified
amino acid; a keto containing amino acid; amino acids comprising
polyethylene glycol or polyether; a heavy atom substituted amino
acid; a chemically cleavable or photocleavable amino acid; an amino
acid with an elongated side chain; an amino acid containing a toxic
group; a sugar substituted amino acid, e.g., a sugar substituted
serine or the like; a carbon-linked sugar-containing amino acid; a
redox-active amino acid; an .alpha.-hydroxy containing acid; an
amino thio acid containing amino acid; an .alpha.,.alpha.
disubstituted amino acid; a .beta.-amino acid; and a cyclic amino
acid other than proline.
[0041] Exemplary fluorescent amino acids include, but are not
limited to, L-2-amino-3-(6,7-dimethoxy-4-coumaryl)-propionic acid
(L-Adp); L-(7-hydroxycoumarin-4-yl)ethylglycine; 3-pyrenylalanine
(Pya); .beta.-anthraniloyl-L-.alpha.,.beta.-diaminopropionic acid
(atn Dap) and its derivatives; 3-[2-(phenyl)benzoxazol-5-yl]alanine
derivatives (Box Ala);
4-ethoxymethylene-2-[1]naphtyl-5(4H)oxazolone derivatives; coumaryl
amino acids such as (6,7-dimethoxy-4-coumaryl)alanine (Dmca),
(6-methoxy-4-coumaryl)alanine (Mca),
L-(7-hydroxy-4-coumaryl)alanine, L-(7-methoxy-4-coumaryl)alanine,
D-(7-methoxy-4-coumaryl)alanine, L-(6-chloro,
7-hydroxy-4-coumaryl)alanine, L-(7-ethoxy-4-coumaryl)alanine,
L-(5-methoxy, 7-hydroxy-4-coumaryl)alanine,
L-(5,7-dimethoxy-4-coumaryl)alanine,
L-(5,7-dihydroxy-4-coumaryl)alanine,
L-(6,7-dimethoxy-4-coumaryl)alanine, L-(5-hydroxy,
7-methoxy-4-coumaryl)alanine, and
L-(7-methoxy-4-coumaryl)ethylglycine (CUM).
[0042] "Protein" or "polypeptide" refers to any polymer of two or
more individual amino acids (whether or not naturally occurring)
linked via a peptide bond, and occurs when the carboxyl carbon atom
of the carboxylic acid group bonded to the -carbon of one amino
acid (or amino acid residue) becomes covalently bound to the amino
nitrogen atom of amino group bonded to the -carbon of an adjacent
amino acid. The term "protein" is understood to include the terms
"polypeptide" and "peptide" (which, at times may be used
interchangeably herein) within its meaning. In addition, proteins
comprising multiple polypeptide subunits (e.g., DNA polymerase III,
RNA polymerase II) or other components (for example, an RNA
molecule, as occurs in telomerase) will also be understood to be
included within the meaning of "protein" as used herein. Similarly,
fragments of proteins and polypeptides are also within the scope of
the invention and may be referred to herein as "proteins."
[0043] A particular amino acid sequence of a given protein (i.e.,
the polypeptide's "primary structure," when written from the
amino-terminus to carboxy-terminus) is determined by the nucleotide
sequence of the coding portion of a mRNA, which is in turn
specified by genetic information, typically genomic DNA (including
organelle DNA, e.g., mitochondrial or chloroplast DNA). Thus,
determining the sequence of a gene assists in predicting the
primary sequence of a corresponding polypeptide and more particular
the role or activity of the polypeptide or proteins encoded by that
gene or polynucleotide sequence.
[0044] "Polynucleotide" or "nucleic acid sequence" refers to a
polymeric form of nucleotides. In some instances a polynucleotide
refers to a sequence that is not immediately contiguous with either
of the coding sequences with which it is immediately contiguous
(one on the 5' end and one on the 3' end) in the naturally
occurring genome of the organism from which it is derived. The term
therefore includes, for example, a recombinant DNA which is
incorporated into a vector; into an autonomously replicating
plasmid or virus; or into the genomic DNA of a prokaryote or
eukaryote, or which exists as a separate molecule (e.g., a cDNA)
independent of other sequences. The nucleotides of the invention
can be ribonucleotides, deoxyribonucleotides, or modified forms of
either nucleotide. A polynucleotides as used herein refers to,
among others, single- and double-stranded DNA, DNA that is a
mixture of single- and double-stranded regions, single- and
double-stranded RNA, and RNA that is mixture of single- and
double-stranded regions, hybrid molecules comprising DNA and RNA
that may be single-stranded or, more typically, double-stranded or
a mixture of single- and double-stranded regions.
[0045] "Isolated polypeptide" refers to a polypeptide which is
separated from other contaminants that naturally accompany it,
e.g., protein, lipids, and polynucleotides. The term embraces
polypeptides which have been removed or purified from their
naturally-occurring environment or expression system (e.g., host
cell or in vitro synthesis).
[0046] "Substantially pure polypeptide" refers to a composition in
which the polypeptide species is the predominant species present
(i.e., on a molar or weight basis it is more abundant than any
other individual macromolecular species in the composition), and is
generally a substantially purified composition when the object
species comprises at least about 50 percent of the macromolecular
species present by mole or % weight. Generally, a substantially
pure polypeptide composition will comprise about 60% or more, about
70% or more, about 80% or more, about 90% or more, about 95% or
more, and about 98% or more of all macromolecular species by mole
or % weight present in the composition. In some embodiments, the
object species is purified to essential homogeneity (i.e.,
contaminant species cannot be detected in the composition by
conventional detection methods) wherein the composition consists
essentially of a single macromolecular species. Solvent species,
small molecules (<500 Daltons), and elemental ion species are
not considered macromolecular species.
[0047] "Forster resonance energy transfer" or "FRET" occurs when
excitation energy is transferred between a donor chromophore (or
fluorophore) that has absorbed a photon and an acceptor moiety,
causing quenching of donor electromagnetic radiation elicited from
the donor chromophore (or fluorophore). If the acceptor moiety is a
chromophore (or fluorophore) whose excitation spectra overlaps with
the emissions spectra of the donor, the acceptor moiety will emit
electromagnetic radiation at its characteristic emissions
wavelength. If the acceptor moiety is a not a chromophore (or
fluorophore), it will quench the electromagnetic radiation of the
donor chromophore (or fluorophore) without emitting any of its own
electromagnetic radiation. In this case the acceptor moiety is a
chromophore (or fluorophore) quencher.
[0048] As used herein, a "donor chromophore (or fluorophore)" is a
chromophore (or fluorophore) that, upon absorbing light or other
energy, can transfer excitation energy to an acceptor chromophore
(or fluorophore) or a chromophore (or fluorophore) quencher. This
energy transfer can occur when the absorption spectrum of an
acceptor chromophore (or fluorophore) overlaps the emissions
spectrum of the donor chromophore (or fluorophore). These changes
in emission either by the donor or a combination of the donor and
acceptor can be detected using various known detection methods
(e.g., fluorescent cameras, luminescence, light absorbing
materials, CCD cameras and the like). In one aspect, an fluorescent
amino acid comprises a chromophore (or fluorophore) moiety. In yet
another aspect, a polypeptide comprises at least one fluorescent
amino acid comprising a donor chromophore (or fluorophore) and at
least one fluorescent amino acid comprising an acceptor or quencher
chromophore (or fluorophore).
[0049] A "FRET pair" refers to a donor chromophore (or fluorophore)
moiety and an acceptor chromophore (or fluorophore) moiety, where
the donor, when exposed to an appropriate excitation wavelength,
can transfer excitation energy to the acceptor moiety. This process
is dependent on the distance between donor and acceptor moieties or
a donor and a quencher moiety and requires that the absorption
spectrum of the acceptor or quencher overlaps the emissions
spectrum of the donor. The two members of a FRET pair can be
referred to as a FRET pair.
[0050] As the distance changes between a FRET pair the emission
spectra changes. Typically, a FRET pair are capable of effecting
one another when the distance between them are between about 10 and
80 nm, typically about 10-50, and most commonly about 20-30 nm. As
the distance between the FRET pair increases the drop in the
emission wavelength of an acceptor moiety will be reduced or the
emission spectra of the donor (where the acceptor is a quencher)
will increase. Accordingly, using such changes in emission spectra
one can determine distances between, for example, an amino acid in
a single polypeptide or the distances between an amino acid in a
polypeptide and one in a binding ligand, substrate or the like. In
this way, inhibitors that bind to a particular target site on a
polypeptide can be detected using changes in emission spectra.
[0051] As mentioned above, the efficiency of FRET is dependent on
the separation distance and the orientation of the donor and
acceptor moieties, as described by the Forster equation, the
fluorescent quantum yield of the donor moiety and the energetic
overlap with the acceptor moiety. Forster derived the relationship:
E=(F.sup.0-F)/F.sup.0=R.sub.0.sup.6/(R.sup.6+R.sub.0.sup.6), where
E is the efficiency of FRET, F and F.sup.0 are the fluorescence
intensities of the donor in the presence and absence of the
acceptor, respectively, and R is the distance between the donor and
the acceptor. R.sub.0, the distance at which the energy transfer
efficiency is 50%, is given (nm) by
R.sub.0=9.79.times.10.sup.3(K.sup.2QJn.sup.-4).sup.1/6, where
K.sup.2 is an orientation factor having an average value close to
0.67 for freely mobile donors and acceptors, Q is the quantum yield
of the unquenched fluorescent donor, n is the refractive index of
the intervening medium, and J is the overlap integral, which
expresses in quantitative terms the degree of spectral overlap,
J=.intg.
.sub.0.epsilon..sub..lamda.F.sub..lamda..lamda..sup.4d.lamda./.intg.
.sub.0F.sub..lamda.d.lamda. where .epsilon..sub..lamda. is the
molar absorptivity of the acceptor in M.sup.-1cm.sup.-1 and
F.sub..lamda. is the donor fluorescence at wavelength 1 measured in
cm. Forster, T. (1948) Ann. Physik 2:55-75. Tables of spectral
overlap integrals are readily available to those working in the
field (for example, Berlman, I. B. Energy transfer parameters of
aromatic compounds, Academic Press, New York and London
(1973)).
[0052] The characteristic distance R.sub.0 at which FRET is 50%
efficient depends on the quantum yield of the donor i.e., the
shorter-wavelength fluorophore, the extinction coefficient of the
acceptor, i.e., the longer-wavelength fluorophore, and the overlap
between the donor's emission spectrum and the acceptor's excitation
spectrum.
[0053] Accordingly, Forster resonance energy transfer (FRET) occurs
between two adjacent fluorophores when their distance is small
(e.g., 1-10 nm) and the emission spectrum of one fluorophore has
more than 30% overlapping with the excitation spectrum of the
other. FRET results in the quenching of the donor fluorophore and
excitation of the acceptor fluorophore. Because the efficiency of
energy transfer is highly dependent (sixth-power) on the distance
between donor and acceptor fluorophores, FRET-based techniques have
been extensively used in biological research including
identification of protein interactions, real-time monitoring of
intracellular signaling activities, and high-throughput screening
of bioactive chemicals. The green fluorescent protein (GFP)
variants are the most commonly used fluorophores to label the
target proteins in FRET-based assays and they are powerful probes
for protein localizations and interactions. However, the
fluorescent protein also possesses certain disadvantages. The
labeling is limited to the N- or C-terminus of target proteins, and
the bulky size of these fluorescent proteins sometimes interferes
with the normal function of target proteins because of spatial
hindrance. In terms of FRET-based assays, the flexibility of
fluorescent protein labels also desensitizes the detection of the
change of donor-acceptor distance. Fluorescent amino acids offer
unique advantages in that it not only can they be incorporated into
proteins in a highly specific manner but the rigidity of their
small side chain groups also enhances the sensitivity of FRET-based
assays without perturbing protein functions.
[0054] The disclosure provides peptides, polypeptide or proteins
comprising at least two fluorescent amino acids that are capable of
undergoing FRET. In one embodiment, the peptide, polypeptide or
protein comprises a first fluorescent amino acid comprising a
coumarin fluorescent amino acid and a quencher amino acid having a
general structure I:
##STR00006##
wherein n is any integer between 1 and 10 inclusive (e.g., 1, 2, 3,
4, 5 etc.) and R.sub.1 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo. In yet a further embodiment, the coumarin fluorescent amino
acid has a general structure II:
##STR00007##
wherein n is any integer between 1 and 10 inclusive (e.g., 1, 2, 3,
4, 5 etc.) and R.sub.1 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.1 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring; R.sub.2 is selected from the
group consisting of: H, aryl, substituted aryl, alkyl, substituted
alkyl, carboxyl, aminocarbonyl, alkylsulfonylaminocarboxyl,
alkoxycarbonyl, and halo, or R.sub.2 and R.sub.1, together with the
carbons to which they are bound, can be joined to form a 4 to 7
membered ring or a substituted 4 to 7 membered ring, or R.sub.2 and
R.sub.3, together with the carbons to which they are bound, can be
joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring; R.sub.3 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.3 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring, or R.sub.3 and R.sub.4, together
with the carbons to which they are bound, can be joined to form a 4
to 7 membered ring or a substituted 4 to 7 membered ring; R.sub.4
is selected from the group consisting of: H, aryl, substituted
aryl, alkyl, substituted alkyl, carboxyl, aminocarbonyl,
alkylsulfonylaminocarboxyl, alkoxycarbonyl, and halo, or R.sub.4
and R.sub.3, together with the carbons to which they are bound, can
be joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring. In yet another embodiment, the coumarin fluorescent
amino acid comprises a general structure III:
##STR00008##
wherein R.sub.1 is selected from the group consisting of: H, aryl,
substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.1 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring; R.sub.2 is selected from the
group consisting of: H, aryl, substituted aryl, alkyl, substituted
alkyl, carboxyl, aminocarbonyl, alkylsulfonylaminocarboxyl,
alkoxycarbonyl, and halo, or R.sub.2 and R.sub.1, together with the
carbons to which they are bound, can be joined to form a 4 to 7
membered ring or a substituted 4 to 7 membered ring, or R.sub.2 and
R.sub.3, together with the carbons to which they are bound, can be
joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring; R.sub.3 is selected from the group consisting of: H,
aryl, substituted aryl, alkyl, substituted alkyl, carboxyl,
aminocarbonyl, alkylsulfonylaminocarboxyl, alkoxycarbonyl, and
halo, or R.sub.3 and R.sub.2, together with the carbons to which
they are bound, can be joined to form a 4 to 7 membered ring or a
substituted 4 to 7 membered ring, or R.sub.3 and R.sub.4, together
with the carbons to which they are bound, can be joined to form a 4
to 7 membered ring or a substituted 4 to 7 membered ring; R.sub.4
is selected from the group consisting of: H, aryl, substituted
aryl, alkyl, substituted alkyl, carboxyl, aminocarbonyl,
alkylsulfonylaminocarboxyl, alkoxycarbonyl, and halo, or R.sub.4
and R.sub.3, together with the carbons to which they are bound, can
be joined to form a 4 to 7 membered ring or a substituted 4 to 7
membered ring. In a specific embodiment, the peptide comprises a
coumarin fluorescent amino acid comprising the structure IV:
##STR00009##
and a quenching fluorescent amino acid comprising the general
structure V:
##STR00010##
[0055] In yet another embodiment, the polypeptide comprises a
sequence containing a structure selected from I or V within about
1-15 (e.g., 1-10 nm, 2-8 nm etc.) of a fluorescent amino acid
selected from the group consisting of II, III, or IV. In yet
another embodiment, the fluorescent coumarin amino acid and
quencher amino acid are space about 2, 3, 4, 5, 6, 7, 8, 9, or 10
amino acids from each other.
[0056] It will also be recognized that the fluorophore pairs of the
disclosure are useful not just in peptide, polypeptide and protein
assays, but can also be used in other biological molecules such as
lipids, nucleic acids and the like, where intra- or inter molecule
interactions occurs. Also, the fluorophores can be used in
combination with solid substrates including beads, nanoparticles,
slides, tissue culture systems and the like.
[0057] Alkyl groups include straight-chain, branched and cyclic
alkyl groups. Alkyl groups include those having from 1 to 20 carbon
atoms. Alkyl groups include small alkyl groups having 1 to 3 carbon
atoms. Alkyl groups include medium length alkyl groups having from
4-10 carbon atoms. Alkyl groups include long alkyl groups having
more than 10 carbon atoms, particularly those having 10-20 carbon
atoms. Cyclic alkyl groups include those having one or more rings.
Cyclic alkyl groups include those having a 3-, 4-, 5-, 6-, 7-, 8-,
9- or 10-member carbon ring and particularly those having a 3-, 4-,
5-, 6-, or 7-member ring. The carbon rings in cyclic alkyl groups
can also carry alkyl groups. Cyclic alkyl groups can include
bicyclic and tricyclic alkyl groups. Alkyl groups optionally
include substituted alkyl groups. Substituted alkyl groups include
among others those which are substituted with aryl groups, which in
turn can be optionally substituted. Specific alkyl groups include
methyl, ethyl, n-propyl, iso-propyl, cyclopropyl, n-butyl, s-butyl,
t-butyl, cyclobutyl, n-pentyl, branched-pentyl, cyclopentyl,
n-hexyl, branched hexyl, and cyclohexyl groups, all of which are
optionally substituted. The term cyclopentyl ring refers to a ring
of five carbons with any degree of unsaturation. The term
cyclohexyl ring refers to a ring of six carbons with any degree of
unsaturation.
[0058] Alkenyl groups include straight-chain, branched and cyclic
alkenyl groups. Alkenyl groups include those having 1, 2 or more
double bonds and those in which two or more of the double bonds are
conjugated double bonds. Alkenyl groups include those having from 2
to 20 carbon atoms. Alkenyl groups include small alkyl groups
having 2 to 3 carbon atoms. Alkenyl groups include medium length
alkenyl groups having from 4-10 carbon atoms. Alkenyl groups
include long alkenyl groups having more than 10 carbon atoms,
particularly those having 10-20 carbon atoms. Cyclic alkenyl groups
include those having one or more rings. Cyclic alkenyl groups
include those in which a double bond is in the ring or in an
alkenyl group attached to a ring. Cyclic alkenyl groups include
those having a 3-, 4-, 5-, 6-, 7-, 8-, 9- or 10-member carbon ring
and particularly those having a 3-, 4-, 5-, 6- or 7-member ring.
The carbon rings in cyclic alkenyl groups can also carry alkyl
groups. Cyclic alkenyl groups can include bicyclic and tricyclic
alkyl groups. Alkenyl groups are optionally substituted.
Substituted alkenyl groups include among others those which are
substituted with alkyl or aryl groups, which groups in turn can be
optionally substituted. Specific alkenyl groups include ethenyl,
prop-1-enyl, prop-2-enyl, cycloprop-1-enyl, but-1-enyl, but-2-enyl,
cyclobut-1-enyl, cyclobut-2-enyl, pent-1-enyl, pent-2-enyl,
branched pentenyl, cyclopent-1-enyl, hex-1-enyl, branched hexenyl,
cyclohexenyl, all of which are optionally substituted.
[0059] Aryl groups include groups having one or more 5- or 6-member
aromatic or heteroaromatic rings. Aryl groups can contain one or
more fused aromatic rings. Heteroaromatic rings can include one or
more N, O, or S atoms in the ring. Heteroaromatic rings can include
those with one, two or three N, those with one or two 0, and those
with one or two S. Aryl groups are optionally substituted.
Substituted aryl groups include among others those which are
substituted with alkyl or alkenyl groups, which groups in turn can
be optionally substituted. Specific aryl groups include phenyl
groups, biphenyl groups, pyridinyl groups, and naphthyl groups, all
of which are optionally substituted.
[0060] Arylalkyl groups are alkyl groups substituted with one or
more aryl groups wherein the alkyl groups optionally carry
additional substituents and the aryl groups are optionally
substituted. Specific alkylaryl groups are phenyl-substituted alkyl
groups, e.g., phenylmethyl groups.
[0061] Alkylaryl groups are aryl groups substituted with one or
more alkyl groups wherein the alkyl groups optionally carry
additional substituents and the aryl groups are optionally
substituted. Specific alkylaryl groups are alkyl-substituted phenyl
groups such as methylphenyl.
[0062] The rings that may be formed from two or more of R1-R4
together can be optionally substituted cycloalkyl groups,
optionally substituted cycloalkenyl groups or aromatic groups. The
rings may contain 3, 4, 5, 6, 7 or more carbons. The rings may be
heteroaromatic in which one, two or three carbons in the aromatic
ring are replaced with N, O or S. The rings may be heteroalkyl or
heteroalkenyl, in which one or more CH.sub.2 groups in the ring are
replaced with O, N, NH, or S.
[0063] Optional substitution of any alkyl, alkenyl and aryl groups
includes substitution with one or more of the following
substituents: halogens, --CN, --COOR, --OR, --COR, --OCOOR,
--CON(R).sub.2, --OCON(R).sub.2, --N(R).sub.2, --NO.sub.2, --SR,
--SO.sub.2R, --SO.sub.2N(R).sub.2 or --SOR groups. Optional
substitution of alkyl groups includes substitution with one or more
alkenyl groups, aryl groups or both, wherein the alkenyl groups or
aryl groups are optionally substituted. Optional substitution of
alkenyl groups includes substitution with one or more alkyl groups,
aryl groups, or both, wherein the alkyl groups or aryl groups are
optionally substituted. Optional substitution of aryl groups
includes substitution of the aryl ring with one or more alkyl
groups, alkenyl groups, or both, wherein the alkyl groups or
alkenyl groups are optionally substituted.
[0064] Optional substituents for alkyl, alkenyl and aryl groups
include among others:
--COOR where R is a hydrogen or an alkyl group or an aryl group and
more specifically where R is methyl, ethyl, propyl, butyl, or
phenyl groups all of which are optionally substituted; --COR where
R is a hydrogen, or an alkyl group or an aryl groups and more
specifically where R is methyl, ethyl, propyl, butyl, or phenyl
groups all of which groups are optionally substituted;
--CON(R).sub.2 where each R, independently of each other R, is a
hydrogen or an alkyl group or an aryl group and more specifically
where R is methyl, ethyl, propyl, butyl, or phenyl groups all of
which groups are optionally substituted; R and R can form a ring
which may contain one or more double bonds; --OCON(R).sub.2 where
each R, independently of each other R, is a hydrogen or an alkyl
group or an aryl group and more specifically where R is methyl,
ethyl, propyl, butyl, or phenyl groups all of which groups are
optionally substituted; R and R can form a ring which may contain
one or more double bonds; --N(R).sub.2 where each R, independently
of each other R, is a hydrogen, or an alkyl group, acyl group or an
aryl group and more specifically where R is methyl, ethyl, propyl,
butyl, or phenyl or acetyl groups all of which are optionally
substituted; or R and R can form a ring which may contain one or
more double bonds. --SR, --SO.sub.2R, or --SOR where R is an alkyl
group or an aryl groups and more specifically where R is methyl,
ethyl, propyl, butyl, phenyl groups all of which are optionally
substituted; for --SR, R can be hydrogen; --OCOOR where R is an
alkyl group or an aryl groups; --SO.sub.2N(R).sub.2 where R is a
hydrogen, an alkyl group, or an aryl group and R and R can form a
ring; --OR where R=H, alkyl, aryl, or acyl; for example, R can be
an acyl yielding --OCOR* where R* is a hydrogen or an alkyl group
or an aryl group and more specifically where R* is methyl, ethyl,
propyl, butyl, or phenyl groups all of which groups are optionally
substituted.
[0065] Specific substituted alkyl groups include haloalkyl groups,
particularly trihalomethyl groups and specifically trifluoromethyl
groups. Specific substituted aryl groups include mono-, di-, tri,
tetra- and pentahalo-substituted phenyl groups; mono-, di-, tri-,
tetra-, penta-, hexa-, and hepta-halo-substituted naphthalene
groups; 3- or 4-halo-substituted phenyl groups, 3- or
4-alkyl-substituted phenyl groups, 3- or 4-alkoxy-substituted
phenyl groups, 3- or 4-RCO-substituted phenyl, 5- or
6-halo-substituted naphthalene groups. More specifically,
substituted aryl groups include acetylphenyl groups, particularly
4-acetylphenyl groups; fluorophenyl groups, particularly
3-fluorophenyl and 4-fluorophenyl groups; chlorophenyl groups,
particularly 3-chlorophenyl and 4-chlorophenyl groups; methylphenyl
groups, particularly 4-methylphenyl groups, and methoxyphenyl
groups, particularly 4-methoxyphenyl groups.
[0066] A polypeptide or peptide comprising a FRET pair of
fluorescent amino acids is provided. In one embodiment, the peptide
or polypeptide may be a ligand or a substrate. For example, the
substrate may be a protease substrate or other enzymatic substrate
(e.g., a ligase substrate). In certain embodiment, the substrate
may comprise one or more FRET pairs at different locations so long
as the pairs are in a proximity to undergo FRET (e.g., about 1 to
about 10 nm--1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15
nm). In a specific embodiment the pair comprise a coumarin
fluorescent amino acid and an NBD amino acid or derivative
thereof.
[0067] A polypeptide or peptide comprising a FRET pair of
fluorescent amino acids as described herein may be operably linked
or fused to an additional peptide or polypeptide. For example, cell
penetrating peptides (CPPs) can be used to promote uptake of a
synthesized peptide of the disclosure.
[0068] A CPP comprises an amino acid sequences having a strong
alpha helical structure with arginine (Arg) residues down the
helical cylinder. In yet another embodiment, the CPP domain
comprises a peptide represented by the following general formula:
B.sub.1-X.sub.1-X.sub.2-X.sub.3-B.sub.2-X.sub.4-X.sub.5-B.sub.3
(SEQ ID NO:2) wherein B.sub.1, B.sub.2, and B.sub.3 are each
independently a basic amino acid, the same or different; and
X.sub.1, X.sub.2, X.sub.3, X.sub.4 and X.sub.5 are each
independently an alpha-helix enhancing amino acid, the same or
different. In another embodiment, the CPP domain is represented by
the following general formula:
B.sub.1-X.sub.1-X.sub.2-B.sub.2-B.sub.3-X.sub.3-X.sub.4-B.sub.4
(SEQ ID NO:3) wherein B.sub.1, B.sub.2, B.sub.3, and B.sub.4 are
each independently a basic amino acid, the same or different; and
X.sub.1, X.sub.2, X.sub.3, and X.sub.4 are each independently an
alpha-helix enhancing amino acid the same or different.
[0069] Additionally CPP domains comprise basic residues, e.g.,
lysine (Lys) or arginine (Arg), and further including at least one
proline (Pro) residue sufficient to introduce "kinks" into the
domain. Examples of such domains include the transduction domains
of prions. For example, such a peptide comprises KKRPKPG (SEQ ID
NO:4).
[0070] In one embodiment, the domain is a peptide represented by
the following sequence: X-X-R-X-(P/X)-(B/X)-B-(P/X)-X-B-(B/X) (SEQ
ID NO:5), wherein X is any alpha helical promoting residue such as
alanine; P/X is either proline or X as previously defined; B is a
basic amino acid residue, e.g., arginine (Arg) or lysine (Lys); R
is arginine (Arg) and B/X is either B or X as defined above.
[0071] In another embodiment the CPP is cationic and consists of
between 7 and 10 amino acids and has the formula
K-X.sub.1-R-X.sub.2-X.sub.1 (SEQ ID NO:6) wherein X.sub.1 is R or K
and X.sub.2 is any amino acid. An example of such a peptide
comprises RKKRRQRRR (SEQ ID NO:7).
[0072] Additional transducing domains include a TAT fragment that
comprises at least amino acids 49 to 56 of TAT up to about the
full-length TAT sequence. A TAT fragment may include one or more
amino acid changes sufficient to increase the alpha-helicity of the
fragment. In some instances, the amino acid changes introduced will
involve adding a recognized alpha-helix enhancing amino acid.
Alternatively, the amino acid changes will involve removing one or
more amino acids from the TAT fragment that impede alpha helix
formation or stability. In a more specific embodiment, the TAT
fragment will include at least one amino acid substitution with an
alpha-helix enhancing amino acid. Typically a TAT fragment or other
CPPs will be made by standard peptide synthesis techniques although
recombinant DNA approaches may be used in some cases.
[0073] Fluorescent amino acids can be incorporated into a peptide
or polypeptide using chemical synthesis techniques or through
expression in an appropriate system that allows for incorporation
of the amino acid using tRNA's capable of utilizing such unnatural
amino acids.
[0074] Polypeptide comprising fluorescent amino acids can be
synthesized by commonly used methods such as those that include
t-BOC or FMOC protection of alpha-amino groups. Both methods
involve stepwise synthesis in which a single amino acid is added at
each step starting from the C terminus of the peptide (See,
Coligan, et al., Current Protocols in Immunology, Wiley
Interscience, 1991, Unit 9). Such polypeptides can also be
synthesized by the well known solid phase peptide synthesis methods
such as those described by Merrifield, J. Am. Chem. Soc., 85:2149,
1962; and Stewart and Young, Solid Phase Peptides Synthesis,
Freeman, San Francisco, 1969, pp. 27-62, using a
copoly(styrene-divinylbenzene) containing 0.1-1.0 mmol amines/g
polymer. On completion of chemical synthesis, the peptide or
polypeptide can be deprotected and cleaved from the polymer by
treatment with liquid HF-10% anisole for about 1/4-1 hours at
0.degree. C. After evaporation of the reagents, the peptides are
extracted from the polymer with a 1% acetic acid solution, which is
then lyophilized to yield the crude material. The peptide or
polypeptide can be purified by such techniques as gel filtration on
Sephadex G-15 using 5% acetic acid as a solvent. Lyophilization of
appropriate fractions of the column eluate yield homogeneous
peptide or polypeptide, which can then be characterized by standard
techniques such as amino acid analysis, thin layer chromatography,
high performance liquid chromatography, ultraviolet absorption
spectroscopy, molar rotation, or measuring solubility.
[0075] Biosynthetic methods that employ chemically modified
aminoacyl-tRNAs have been used to incorporate several biophysical
probes into proteins (e.g., Brunner, J. New Photolabeling and
crosslinking methods, Annu. Rev Biochem, 483-514 (1993); and,
Krieg, U. C., Walter, P., Hohnson, A. E. Photocrosslinking of the
signal sequence of nascent preprolactin of the 54-kilodalton
polypeptide of the signal recognition particle, Proc. Natl. Acad.
Sci, 8604-8608 (1986)).
[0076] It has been shown that fluorescent amino acids can be
site-specifically incorporated into proteins in vitro by the
addition of chemically aminoacylated suppressor tRNAs to protein
synthesis reactions programmed with a gene containing a desired
amber nonsense mutation. Using these approaches, one can substitute
a number of the common twenty amino acids with close structural
homologues, e.g., fluorophenylalanine for phenylalanine, using
strains auxotrophic for a particular amino acid. See, e.g., Noren,
C. J., Anthony-Cahill, Griffith, M. C., Schultz, P. G. A general
method for site-specific incorporation of fluorescent amino acids
into proteins, Science, 244: 182-188 (1989); M. W. Nowak, et al.,
Science 268:439-42 (1995); Bain, J. D., Glabe, C. G., Dix, T. A.,
Chamberlin, A. R., Diala, E. S. Biosynthetic site-specific
Incorporation of a non-natural amino acid into a polypeptide, J. Am
Chem Soc, 111:8013-8014 (1989); N. Budisa et al., FASEB J. 13:41-51
(1999); Ellman, J. A., Mendel, D., Anthony-Cahill, S., Noren, C.
J., Schultz, P. G. Biosynthetic method for introducing fluorescent
amino acids site-specifically into proteins, Methods in Enz.,
301-336 (1992); and, Mendel, D., Cornish, V. W. & Schultz, P.
G. Site-Directed Mutagenesis with an Expanded Genetic Code, Annu
Rev Biophys. Biomol Struct. 24, 435-62 (1995); Isabelle Dufau,
Honore Mazarguil, Design of a fluorescent amino acid derivative
usable in peptide synthesis Tetrahedron Letters, 41:6063-6066,
2000).
[0077] For example, a suppressor tRNA can be prepared to recognize
the stop codon UAG and was chemically aminoacylated with a
fluorescent amino acid. Conventional site-directed mutagenesis can
be used to introduce the stop codon TAG, at the site of interest in
a coding sequence. See, e.g., Sayers, J. R., Schmidt, W. Eckstein,
F. 5', 3'Exonuclease in phosphorothioate-based
oligonucleotide-directed mutagenesis, Nucleic Acids Res, 791-802
(1988). When the acylated suppressor tRNA and the mutant gene are
combined in an in vitro transcription/translation system, the
fluorescent amino acid is incorporated in response to the UAG codon
which results in a protein containing that amino acid at the
specified position.
[0078] Microinjection techniques can also be used to incorporate
fluorescent amino acids into proteins. See, e.g., Nowak et al.,
Science, 268:439 (1995) and D. A. Dougherty, Curr. Opin. Chem.
Biol., 4:645 (2000). For example, a cell can be injected with an
mRNA encoding a target protein with a UAG stop codon at the amino
acid position of interest and an amber suppressor tRNA
aminoacylated with the desired fluorescent amino acid. The
translational machinery of the cell then inserts the fluorescent
amino acid at the position specified by the UAG codon. Examples
include the incorporation of a fluorescent amino acid into
tachykinin neurokinin-2 receptor to measure distances by
fluorescence resonance energy transfer, see, e.g., G. Turcatti, K.
Nemeth, M. D. Edgerton, U. Meseth, F. Talabot, M. Peitsch, J.
Knowles, H. Vogel and A. Chollet, J. Biol. Chem., 271:19991 (1996);
the incorporation of biotinylated amino acids to identify
surface-exposed residues in ion channels, see, e.g., J. P.
Gallivan, H. A. Lester and D. A. Dougherty, Chem. Biol., 4:739
(1997); the use of caged tyrosine analogs to monitor conformational
changes in an ion channel in real time, see, e.g., J. C. Miller, S.
K. Silverman, P. M. England, D. A. Dougherty and H. A. Lester,
Neuron, 20:619 (1998); and, the use of alpha hydroxy amino acids to
change ion channel backbones for probing their gating mechanisms.
See, e.g., P. M. England, Y. Zhang, D. A. Dougherty and H. A.
Lester, Cell, 96:89 (1999); and, T. Lu, A. Y. Ting, J. Mainland, L.
Y. Jan, P. G. Schultz and J. Yang, Nat. Neurosci., 4:239
(2001).
[0079] The ability to include fluorescent amino acids with various
sizes, acidities, nucleophilicities, hydrophobicities, and other
properties into proteins can greatly expand the ability to
rationally and systematically manipulate the structures of proteins
and probe protein function.
[0080] The disclosure contemplates the use of polypeptide
comprising fluorescent amino acids and a combination of both
natural and fluorescent amino acids. Techniques for the
incorporation of fluorescent amino acid in vivo have been
developed. For example, an organism or system comprising an
orthogonal tRNA (O-tRNA) and an orthogonal aminoacyl tRNA
synthetase (O-RS) can be used. Typically, the O-RS preferentially
aminoacylates the O-tRNA with at least one fluorescent amino acid
in the translation system and the O-tRNA recognizes at least one
selector codon. The translation system thus inserts the fluorescent
amino acid into a protein produced in the system, in response to an
encoded selector codon.
[0081] A translation systems includes both cells, such as bacterial
cells (e.g., Escherichia coli), archeaebacterial cells, eukaryotic
cells (e.g., yeast cells, mammalian cells, plant cells, insect
cells), as well as cell-free system (e.g., an in vitro translation
system, such as a translation extract from a cellular extract).
[0082] Any of a codons can be used to incorporate an fluorescent
amino acid including nonsense codons, rare codons, four (or more)
base codons, or the like. In one embodiment, codon is an amber
codon, or an opal codon, a fluorescent codon, at least a four base
codon or the like. A number of codons can be introduced into a
desired gene.
[0083] The 64 genetic codons code for 20 amino acids and 3 stop
codons. Because only one stop codon is needed for translational
termination, the other two stop codons can in principle be used to
encode nonproteinogenic amino acids. The amber stop codon, UAG, has
been successfully used in in vitro biosynthetic system to direct
the incorporation of fluorescent amino acids. Among the 3 stop
codons, UAG is the least used stop codon in Escherichia coli. Some
Escherichia coli strains contain natural suppressor tRNAs, which
recognize UAG and insert a natural amino acid.
[0084] Codons comprising four or more base codons can also be used
in the disclosure. Examples of four base codons include, for
example, UAGA, CUAG, AGGA, CCCU, and the like. Examples of five
base codons include, e.g., CUAGA, CUACU, AGGAC, CCCCU, CCCUC,
UAGGC, and the like. For example, in the presence of mutated
O-tRNAs such as a special frameshift suppressor tRNAs, with
anticodon loops the four or more base codon is read as single amino
acid.
[0085] Proteins or polypeptides that can be generated are not to be
limited by the disclosure. Any polypeptide capable of detection or
analysis can be used. For example, the protein can be an enzymatic
protein, receptor protein, receptor ligand protein, membrane
protein, secondary messenger proteins, a therapeutic protein and
the like. For example, the protein comprising a FRET pair of
fluorescent amino acids can comprise a polypeptide selected from
the group consisting of a cytokine, erythropoietin (EPO), insulin,
human growth hormone, epithelial Neutrophil Activating Peptide-78,
a growth factor, a growth factor receptor, an interferon, an
interleukin (e.g., IL-1, an IL-2, an IL-3, an IL-4, an IL-5, an
IL-6, an IL-7, an IL-8, an IL-9, an IL-10, an IL-11, an IL-12), a
transcriptional activator, an inflammatory molecule, an oncogene
product, a peptide hormone, a signal transduction molecule, a
steroid hormone receptor, a transcriptional suppressor,
GRO-.alpha., -.beta., -.gamma., -.delta., hepatocyte growth factor,
insulin-like growth factor, leukemia inhibitory factor, oncostatin
M, PD-ECSF, PDGF, pleiotropin, SCF, VEGEF, G-CSF, fibroblast growth
factor, platelet derived growth factor, tumor necrosis factor,
transforming growth faction-.alpha., -.beta., epidermal growth
factor, keratinocyte growth factor, stem cell factor, CD40L/CD40,
VLA-4/VCAM-1, ICAM-1/LFA-1, hyalurin/CD44, Mos, Ras, Raf, Met; p53,
Jun, Myb, Rel, Tat, Fos, Myc, testosterone receptor, estrogen
receptor, progesterone receptor, aldosterone receptor, LDL
receptor, corticosterone, alpha-1 antitrypsin, angiostatin, an
apolipoprotein, an apoprotein, a chemokine, collagen, factor IX,
factor VII, factor VIII, factor X, G-CSF, GM-CSF, serum albumin,
somatostatin, to name but a few.
[0086] A polypeptide comprising a FRET pair of fluorescent amino
acids can contain any number of fluorescent amino acids (e.g., from
1-15 or more). For example, the protein can comprise 1, 2, 3, 4, 5,
6, 7, 6, 9, 10, 11, 12, 13, 14, 15 or more fluorescent amino acids.
The fluorescent amino acids can be the same or different. In one
embodiment, the protein comprises at least two fluorescent amino
acids capable of undergoing FRET. In a specific embodiment, the at
least to fluorescent amino acids capable of undergoing FRET
comprises an NBD or derivative thereof or a CUM or derivative
thereof. In another embodiment, the FRET pair can comprise a G5 and
G6 fluorescent amino acid.
[0087] A translation system can be used to produce a polypeptide
comprising at least one fluorescent amino acid by providing
polynucleotide comprising at least one codon recognized by a tRNA
fluorescent amino acid, wherein the polynucleotide encodes a
protein of interest. The translation system comprises an orthogonal
tRNA (O-tRNA) that functions in the translation system and
recognizes the codon and an orthogonal aminoacyl tRNA synthetase
(O-RS), that aminoacylates the O-tRNA with a fluorescent amino acid
in the translation system. The translation system further comprises
a fluorescent amino acid. Using the methods described herein a
protein comprising a fluorescent amino acids can be produced that
can be stably folded, glycosylated, or otherwise modified.
[0088] The disclosure provides methods, kits and compositions
useful for analyzing protein structure, function and
structure-function relationships. In addition, the disclosure
provides methods useful for identifying binding ligands and
substrates for protein or enzyme. The methods, kits and
compositions of the disclosure utilize, in one embodiment,
fluorescent amino acids that are capable of acting as an acceptor
or donor of electromagnetic radiation (e.g., Forster resonance
energy transfer (FRET)). Using the incorporation of such
fluorescent amino acids FRET techniques can be used to measure the
relationship between amino acids within a single polypeptide (e.g.,
to determine distance between amino acids in an active site), to
measure putative ligand binding, wherein a polypeptide comprises
one fluorescent amino acid in a binding site and the ligand
comprises a different FRET moiety (or vice versa), or a polypeptide
having enzymatic activity with an fluorescent amino acid in the
active site or co-factor site and a FRET moiety within the
substrate (or vice versa).
[0089] In one embodiment, a method of identifying a binding ligand
or substrate for a target polypeptide comprises providing a
polynucleotide comprising at least one codon that results in the
incorporation of at least one fluorescent amino acid upon
translation, wherein the fluorescent amino acid comprises a first
acceptor or donor chromophore moiety; translating the
polynucleotide to obtain a fluorescent polypeptide comprising the
at least one fluorescent amino acid; contacting fluorescent
polypeptide with a putative binding ligand comprising a second
acceptor or donor chromophore moiety, wherein the first and second
acceptor or donor chromophore moieties are different, wherein the
first and second acceptor or donor chromophore moieties are
selected to undergo Forster resonance energy transfer (FRET) when a
binding ligand is bound to a target polypeptide, and identifying
FRET, wherein the presence of FRET is indicative that the putative
binding ligand binds to the target polypeptide thereby identifying
the binding ligand. In one embodiment, the first fluorescent amino
acid is a CUM amino acid or derivative thereof and the second
fluorescent amino acid in the corresponding ligand is a quenching
fluorescent amino acid (e.g., an NBD or derivative thereof).
[0090] In one embodiment, a method of identifying a binding ligand
or substrate for a target polypeptide comprises providing a
polynucleotide comprising at least two codon that results in the
incorporation of at least one fluorescent amino acid upon
translation (e.g., a CUM amino acid or derivative thereof), wherein
the fluorescent amino acid comprises a first fluorophore moiety;
and a second codon that results in the incorporation of a second
quenching fluorophore (e.g., NBD or a derivative thereof);
translating the polynucleotide to obtain a polypeptide comprising
the at least two fluorescent amino acid; contacting the polypeptide
with a putative binding ligand or interacting protein; exciting the
polypeptides with an excitation wavelength and measuring emission
spectra, wherein the presence of FRET is indicative that the
putative binding ligand or interacting protein binds to the target
polypeptide thereby identifying the ligand or substrate.
[0091] The disclosure provides, for example, FRET-based
high-throughput screening for SUMO ligase or protease inhibitors.
SUMO, known as small ubiquitin-related modifier, is a family of
post-translational protein modifiers involved in immune signal
transduction, transcriptional regulation and neurodegenerative
diseases. SUMO undergoes reversible conjugation to the target
protein via the help of SUMO ligases, and this process has been
proven to be required for most eukaryotic organisms. Screening of
small chemical inhibitors of SUMO ligases are important because
small chemicals offer better spatial and temporal control of
SUMOylation process compared with traditional methods such as gene
knockout studies. Incorporating fluorescent amino
acid-L-(7-hydroxycoumarin-4-yl)ethylglycine (CUM) into this
reporter to facilitate the high-throughput screening for SUMO
ligase inhibitors promotes discovery.
[0092] SUMOylation is an important post-translational protein
modification mechanism which plays an important role in a variety
of biological processes. Via the catalysis of multiple enzymes,
SUMO peptides are reversibly conjugated to the lysine resides of
target proteins to modify their localization and functions.
Conjugation and deconjugation of SUMO is a cascade event requiring
multiple protein-protein interactions. SUMO peptides interact with
a series of enzymes including the E1 activating enzyme, E2
conjugating enzyme and E3 ligases. These enzymes also interact with
each other and the target proteins to facilitate the transfer of
SUMO peptides. The nature of the SUMOylation network indicates a
great potential for small chemical inhibitors to be used in the
investigation and manipulation of this important process.
[0093] Using fluorescent proteins to tag protein components
involved in the SUMOylation process successfully detected the
interaction of SUMO with the E2 enzyme and one E3 ligase. The
disclosure provides a FRET-based method to analyze the interaction
between SUMO and other components involved in the SUMOylation
network. The methods and compositions of the disclosure are
applicable to high-throughput screening assay to look for small
chemical inhibitors which can specifically disrupt protein-protein
interactions involved in this network. The small chemical
inhibitors will not only contribute to the investigation of
SUMOylation and improve the knowledge about this important process,
but the work will also provide a novel approach for high-throughput
screening assays targeting protein-protein interactions.
[0094] The disclosure can use both traditional fluorophores,
modified fluorophores or fluorescent amino acids that are capable
of fluorescence. Large fluorescent moieties may result in spatial
hindrance and interference, however, such interference can be
determined empirically. In another aspect, the disclosure can use
fluorescent amino acid with novel side chain groups which can be
genetically encoded and incorporated into proteins with high
specificity to measure protein function and structure. FRET
reporter protein with fluorescent amino acids or fluorescent
moieties to facilitate the high-throughput screening of, for
example, SUMO ligase inhibitors, which will be important in studies
of cytokine signaling pathways.
[0095] Protein post-translational modifications are general
mechanisms that alter protein functions in most cells, especially
in eukaryotic cells. Common modifications involve attachment of
small chemical moieties such as phosphate, acetyl or methyl groups,
which plays a key role in many cellular events including signaling
transduction, DNA repair and transcriptional regulation. Besides
those small chemical moieties, small peptides can also function as
protein modifiers. Ubiquitin, a 76-residue peptide, is a well
studied protein modifier whose covalent modification can result in
proteasome-mediated degradation of target proteins. SUMO, known as
Small Ubiquitin-related MOdifier, has emerged as an important
protein modifier in recent years. Composed of .about.100 amino
acids, SUMO undergoes reversible conjugation to the lysine residues
of target proteins (SUMOylation) via the catalysis of various
enzymes. Although structurally related to ubiquitin, SUMO shares
only 18% sequence identity with ubiquitin and has very different
effects on target proteins. SUMOylation in a target-specific manner
can affect a target protein's intracellular localization, its
ability to interact with other proteins or its transcriptional
activity. SUMOylation may also compete with ubiquitination on the
same lysine residue to increase the stability of target proteins.
Given its important role in many biological processes, SUMO is
required for most eukaryotic organisms. Although not well
understood yet, there have been reports linking misregulated
SUMOylation to some human diseases including neurodegenerative
diseases and viral infection.
[0096] Analogous to ubiquitination, conjugation and deconjugation
of SUMO require the catalysis of multiple enzymes (FIG. 17). SUMO
is translated from mRNA as a precursor protein. Pre-SUMO is then
recognized by SUMO-specific peptidases (SENPs) and cleaved to
generate a C-terminal Gly-Gly motif. The heterodimer Aos1/Uba2,
which is the SUMO E1 activating enzyme, then forms a thioester bond
with SUMO using the energy from the degradation of ATP. SUMO is
further transferred from the E1 enzyme to the active site cysteine
of the SUMO E2 conjugating enzyme Ubc9. Catalyzed by SUMO E3
ligases, SUMO is finally transferred from Ubc9 to the lysine
residue of target proteins. SUMOylated proteins can then be
recognized by SENPs and free SUMO is cleaved off to be used for the
conjugation to other proteins. Protein-protein interactions are
crucial for SUMOylation to proceed. Using X-ray crystallography and
protein-protein interaction assays such as yeast two-hybrid,
interactions between different protein components have been
investigated in the past few years. Cocrystallization of SUMO-E1
showed SUMO interacts with two distinct domains of heterodimer
Aos1/Uba2 to form the thioester bond. Ubc9 possesses several
protein interaction sites for E1, SUMO and E3 ligases and functions
as the core components in the cascade. SUMO E3 ligases interact
with both substrate proteins and Ubc9/SUMO to facilitate transfer
of SUMO by recruitment of substrate proteins.
[0097] As a three-enzyme cascade, SUMOylation involves many enzymes
with different specificities. SUMO itself represents a family of
closely related proteins. Four SUMO isoforms have been identified
in human named as SUMO-1 to SUMO-4. Except SUMO-4 which is only
expressed in the kidney and spleen, all SUMO proteins are
ubiquitously expressed at all developmental stages. While SUMO
isoforms share high sequence identity with each other (50% between
SUMO-1 and SUMO-2, and 95% between SUMO-2 and SUMO-3), these
isoforms are not functionally identical. Conjugation of SUMO2/3 but
not SUMO-1 can be induced in response of certain stresses.
Different SUMO isoforms are also used preferentially to modify
different substrate proteins.
[0098] In contrast to E1 and E2 which have only one isoform in
human, E3 ligases are consisted of three distinct types of
proteins: the PIAS [protein inhibitor of activated STAT (signal
transducer and activator of transcription)] family, the polycomb
group protein Pc2 and the nuclear pore complex protein RanBP2.
Among the three types of E3 ligases, PIAS proteins have been most
extensively studied. Human genome encodes four PIAS genes, PIAS1,
PIAS3, PIASx and PIASy. PIAS proteins share a high sequence
homology. They all feature a SP-RING domain, which is crucial for
binding Ubc9, and a SUMO interaction motif (SIM) implicated in
directly binding SUMOs. PIAS proteins were first identified by
their ability to interact with and inhibit the transcriptional
activity of STAT proteins. PIAS1 and PIAS3 interact with STAT1 and
STAT3 respectively with high specificity. Later it was discovered
that PIAS proteins can also function as SUMO E3 ligases to induce
SUMOylation of the proteins they interact with. In the case of
cytokine signaling pathway, binding of interferon gamma to its
receptor leads to activation of STAT1, which translocates into
nucleus and induces downstream gene expression. PIAS1 interacts
with activated STAT1 and induces SUMOylation of STAT1 to inhibit
its transcriptional activity, therefore ensuring proper regulation
of interferon signaling (FIG. 4). Besides STAT proteins, PIASs can
also promote SUMOylation of a variety of structurally diverse
proteins. Most of these proteins are transcriptional factors
including p53, whose transcriptional activity is strongly repressed
by PIAS1-mediated SUMOylation.
[0099] While SUMOylation plays an important role in many biological
processes including regulation of immune signal transduction,
stabilization of target proteins and maintenance of chromosomal
integrity, the investigation of SUMOylation network in vivo has
been hindered by many challenges. Conjugation and deconjugation of
SUMO is highly dynamic process and SUMO can be quickly removed upon
cell lysis unless cells are lysed in denaturing conditions or
protease inhibitors are added. Furthermore, given the important
roles they play, gene knockout of components in SUMOylation can be
lethal. Depletion of SUMO1 or the E2 enzyme in mice is
embryonically lethal. PIAS1 deficient mice are partially
embryonically lethal and the activity of their interferon-mediated
JAK-STAT pathway is deregulated. To overcome these difficulties,
new tools besides the traditional biochemical and genetic
approaches are needed to study the SUMOylation network.
[0100] Among a variety of techniques for biological research, small
chemical compounds stand as unique tools to manipulate the activity
of biological processes. Compared with other biological approaches,
bioactive small chemical compounds not only offer better spatial
and temporal control of biological processes but also can be used
to investigate the biological function of proteins when gene
knockout studies are not feasible. While the majority of chemical
compounds used in biological research are receptor
agonists/antagonists or enzyme inhibitors, small chemical compounds
disrupting non-enzyme protein-protein interactions have emerged as
useful tools. Nutlin-3, an ubiquitin E3 ligase inhibitor developed
in 2004, has been shown to induce apoptosis and growth inhibition
of cancer cells by disrupting the interaction of ubiquitin E3
ligase MDM2 and its substrate p53. Analogous to ubiquitination,
SUMOylation requires interactions between SUMO, catalyzing enzymes
and substrate proteins. Therefore small chemical compounds
disrupting interactions between components in SUMOylation will be
very useful to dissect the whole network. Currently there is no
available small chemical compound specific for SUMOylation
pathways, which indicates an urgent need in developing
high-throughput screening assays for these small molecule
inhibitors.
[0101] The disclosure also provides methods and compositions using
FRET (Forster resonance energy transfer)-based high-throughput
screening to identify small chemical inhibitors which can
specifically disrupt protein-protein interaction involved in the
SUMOylation network. FRET occurs between two adjacent fluorophores
when their distance is smaller than 1-10 nm and the emission
spectrum of donor has more than 30% overlapping with the excitation
spectrum of acceptor. Energy transferred from excited donor to
acceptor results in quenching of donor and excitation of acceptor
(FIG. 1). Because the efficiency of energy transfer is highly
dependent (sixth-power) on the distance between donor and acceptor
fluorophores, FRET-based techniques have been extensively used in
biological research including identification of protein
interactions, real-time monitoring of intracellular signaling
activities, and high-throughput screening of bioactive molecules.
Compared with traditional techniques used to identify
protein-protein interactions such as co-immunoprecipitation and
yeast two-hybrid, FRET is able to offer real-time monitoring in
living cells and is easier to be adapted into high-throughput
screening. In FRET-based assays, proteins are tagged with different
fluorophores to form FRET pairs. Interaction of proteins recruits
fluorophores together and increase the efficiency of energy
transfer from donor fluorophores to acceptor fluorophores.
Disruption of protein-protein interactions by small chemical
inhibitors will separate the fluorophores apart and result in
decreased FRET efficiency of the system.
Examples
[0102] Construct Mammalian Expression Constructs of FRET Reporter
Protein.
[0103] The expression plasmid expressing chimeric protein
YFP-STAT1-KDJAK1-PIAS1*, and as negative control, YFP-STAT1-PIAS1*
in mammalian cells were constructed in pcDNA3 (Invitrogen). The
kinase domain of JAK1 phosphorylates the STAT1 and the
phosphorylation of STAT1 initiates the interaction between PIAS1
and STAT1. Amber codon* is introduced into different positions of
PIAS1 for later incorporation of
L-(7-hydroxycoumarin-4-yl)ethylglycine. The constructs was
transfected into HEK 293 cells and the fluorescent amino acid
incorporation will be carried out. The cells were excited at 340 nm
and fluorescence emission will be detected at 470 nm (for cells
expressing YFP-STAT1-PIAS1*) or 527 nm (for cells expressing
YFP-STAT1-KDJAK3-PIAS1*) in the fluorescence plate reader, and
cells without transfection are used as negative control.
[0104] Different organic fluorophores can be selected based on
their excitation/emission spectrums and covalently conjugated to
the backbone of amino acids. Orthogonal tRNA/aminoacyl-tRNA
synthetase pairs will be screened. The resulting fluorescent amino
acids will be incorporated into proteins individually and their
FRET efficiency with L-(7-hydroxycoumarin-4-yl)ethylglycine will be
measured.
[0105] As a testing of the developed assay of screening small
molecular inhibitor(s), a pilot screening using the small molecular
compound library containing 10,000 Benzopyran-like molecules will
be performed. More libraries are available from the Genomic
Institute at UCR. The cells will be transfected and spotted into
96- or 384-well plates and incubated for proper time and FRET assay
will be performed. The candidates showing decreased FRET efficiency
will be picked up for further analysis.
[0106] As a testing of the developed assay of screening small
molecular inhibitor(s), a pilot screening using the small molecular
compound library containing 10,000 Benzopyran-like molecules will
be performed. More libraries are available from the Genomic
Institute at UCR. The cells will be transfected and spotted into
96- or 384-well plates and incubated for proper time and FRET assay
will be performed. The candidates showing decreased FRET efficiency
will be picked up for further analysis.
[0107] SUMO1, Ubc9 and PIAS1 have been cloned from human cDNA
library using polymerase chain reactions (PCR).
[0108] Cloning of Genes Encoding Proteins Involved in the
SUMOylation Network into Mammalian Expression Vectors:
[0109] The open reading frames encoding SUMO1-4, SENP1-7 and PIAS1,
3, x, y will be amplified using PCR reactions from human cDNA
library. The PCR products will be cloned into pCRII-TOPO vectors
using the TOPO TA cloning kit (Invitrogen, CA) and sequenced for
clones with correct sequences. The open reading frames of SUMOs
will then be ligated into pCRII vectors encoding CyPet while the
other genes will be ligated into pCRII encoding YPet. The CyPet and
YPet fusion constructs will be transferred to mammalian expression
vectors pcDNA3.1-hygromycin and pcDNA3.1-V5His (Invitrogen, CA)
respectively.
[0110] Transfection of HEK293 Cells and Determination of FRET
Emission Ratio of Transfected Cells:
[0111] 5.times.10.sup.4 per well HEK293 cells will be plated in
12-well tissue culture plate in 0.5 mL Dulbecco's Modified
Essential Medium (DMEM) supplemented with 10% fetal bovine serum
(FBS) (Invitrogen, CA). After overnight incubation the cells will
be transiently cotransfected with 1 ug plasmid encoding a CyPet
fusion protein and 1 ug plasmid encoding a YPet fusion protein
using FuGene6 (Roche, Switzerland) for 24 h in triplicate groups.
Culture medium will then be aspirated and replaced with 50 .mu.L
phosphate buffered saline (PBS). Cells will be scraped off using a
cell scraper (Fisher Scientific, PA) and the cell suspension will
be transferred into a 384-well black/clear plate (BD bioscience,
CA). The plate will be read on our fluorometric high-throughput
plate reader (Flexstation II.sup.384) instrument (Molecular
Devices, CA). Two settings will be used to detect the fluorescence
emitted from transfected cells: excitation at 414 nm with a
long-pass cutoff filter at 455 nm and emission at 475 nm and 530
nm; excitation at 465 nm with a long-pass cutoff filter at 495 nm
and emission scan at 530 nm. The settings are adjusted to excite
and detect at the appropriate wavelengths for each fluorophore. For
example,
FLC.sub.DD: FLC at 465 nm under excitation at 414 nm with a
long-pass cutoff filter at 455 nm; FLC.sub.DA: FLC at 530 nm under
excitation at 414 nm with a long-pass cutoff filter at 455 nm;
FLC.sub.AA: FLC at 530 nm under excitation at 465 nm with a
long-pass cutoff filter at 495 nm;
[0112] The FRET emission ratio (r) was defined to be the ratio of
corrected fluorescence intensities at 530 nm and 475 nm under
excitation at 414 nm:
r=FLC.sub.DA/FLC.sub.DD (1)
[0113] Because energy transfer from the donor fluorophore to the
acceptor fluorophore will result in an increase of r, increased r
can serve as an indication of FRET. A cross-talk constant can be
determined for cells expressing only one type of fluorophore:
a=FLC.sub.DA/FLC.sub.AA (2)
[0114] Then the modified equation of r will be:
r = FLC DA - a .times. FLC AA FLC DD ( 3 ) ##EQU00001##
in which a.times.FLC.sub.AA reflected the direct emission. r will
be determined for different pairs of fluorophores. They will then
be compared with the ratio from the control group in which the
cells will be transfected with plasmids encoding labeled
constructs. The student t test will be used to check if the FRET
emission ratios of tested protein pairs have statistically
significant differences with that from the control group. The
positive pairs showing an increase of r will be subject to further
testing described below.
[0115] Estimation of Protein-Protein Binding Affinities in Living
Cells Using FRET Measurements:
[0116] 5.times.10.sup.4 HEK293 cells will be plated into 12-well
plate and transfected with plasmids encoding the fusion protein
pairs using the protocol described above. After the cells are
suspended and transferred into a 384-well black/clear plate, the
corrected fluorescence intensities of the cells will be determined
in Flexstation II.sup.384. Because of the overlapping of CyPet and
YPet fluorescence spectra, all these intensities are consisted of
three components: the donor (CyPet) fluorescence (I.sub.d), the
sensitized acceptor (YPet) fluorescence due to FRET (I.sub.da), and
the acceptor (YPet) fluorescence (I.sub.a). To isolate these
components, FLC.sub.DD, FLC.sub.DA and FLC.sub.AA from HEK293 cells
expressing only YPet will be measured. The following cross-talk
constants will be determined as:
a = FLC DA FLC AA ##EQU00002## b = FLC DD FLC AA ##EQU00002.2##
[0117] The FLC.sub.DD, FLC.sub.DA and FLC.sub.AA from HEK293 cells
expressing only CyPet can be measured and determine the cross-talk
constants for CyPet:
c = FLC AA FLC DD ##EQU00003## d = FLC DA FLC DD ##EQU00003.2##
[0118] The corrected fluorescence intensities of the transfected
cells will be characterized by the following equations:
FLC DD = I d + ( b a ) I da + bI a ##EQU00004## FLC DA = dI d + I
da + aI a ##EQU00004.2## FLC AA = cI d + ( c d ) I da + I a
##EQU00004.3##
[0119] In these equations I.sub.d refers to the CyPet fluorescence
at 475 nm under excitation of 414 nm. I.sub.da is the FRET-induced
YPet emission at 530 nm under excitation of 414 nm. I.sub.a is the
direct YPet fluorescence at 530 nm under excitation of 465 nm. From
these equations I.sub.d, I.sub.da, and I.sub.a as functions of
FLC.sub.DD, FLC.sub.DA and FLC.sub.AA can be obtained:
I a = ( dFLC AA - cFLC DA ) ( d - ca ) ##EQU00005## I d = ( aFLC DD
- bFLC DA ) ( a - bd ) ##EQU00005.2## I da = FLC DA - aI a - bI b
##EQU00005.3##
[0120] To convert I.sub.d, I.sub.da, and I.sub.a into FRET
efficiency (E) and total concentrations of the donor (D) and the
acceptor (A), two factors need to be determined: 1) The ratio of
sensitized acceptor emission to donor fluorescence quenching (G
factor) and 2) The ratio of donor/acceptor fluorescence intensities
under equimolar concentrations in the absence of FRET (k factor).
After the G and k factors were determined for CyPet and YPet under
our experiment conditions, FRET efficiency E and the concentration
ratio
D A ##EQU00006##
can be determined as:
E = I da G I d + I da G ##EQU00007## D A = I d + I da G I a k
##EQU00007.2##
[0121] I.sub.a is used to present the relative concentration of the
acceptor (A) because I.sub.a is not altered by FRET and is
proportional to the concentration of the donor:
A=I.sub.a
[0122] Then the relative concentration of the donor (D) can be
represented as:
D = I d + I da G k ##EQU00008##
[0123] HEK293 cells will be transfected with varying amount of
plasmids. I.sub.d, I.sub.da and I.sub.a will be calculated for each
batch of transfected cells from FLC.sub.DD, FLC.sub.DA and
FLC.sub.AA determined by Flexstation II.sup.384. E and the
D A ##EQU00009##
will be also calculated to estimate the equilibrium dissociation
constant K.sub.d following the protocol described below.
[0124] The behavior of the bimolecular interaction between donor
and acceptor molecules can be described by the following equations
based on receptor-ligand binding theories:
D free + A free .revreaction. DA ##EQU00010## D = D free + DA
##EQU00010.2## A = A free + DA ##EQU00010.3## Kd = D free A free DA
= ( D - DA ) ( A - DA ) DA ##EQU00010.4##
[0125] D.sub.free, A.sub.free and DA in the equations stand for the
concentrations of free donor, free acceptor and binding complex of
donor-acceptor, respectively. At equilibrium, DA can be represented
as the function of D, A and K.sub.d:
DA = ( A + D + K d ) - ( A + D + K d ) 2 - 4 AD 2 ##EQU00011##
[0126] Then the predicted FRET efficiency E.sub.pred in a
two-molecule system can be described as:
E pred = E max .times. DA D ##EQU00012##
[0127] E.sub.max is defined as the intrinsic FRET efficiency
between a given pair of FRET donor and acceptor which is the FRET
efficiency when all the FRET donor molecules are occupied by the
acceptor molecules. Combining yields:
E pred = E max .times. ( A + D + K d ) - ( A + D + K d ) 2 - 4 AD 2
D ##EQU00013##
[0128] For cells expressing varying amounts of fusion protein
pairs, A and D can be determined based on the methods described
above. Thus two unknown independent variables E.sub.max and K.sub.d
need to be estimated and adjusted to minimize the difference
between the predicted FRET efficiency (E.sub.pred) and
experimentally determined FRET efficiency (E). Assuming E.sub.pred
having a Gaussian distribution, based on maximum likelihood
analysis the best estimation of K.sub.d and E.sub.max results in a
minimized squared residual error (SEE) which is defined as:
SEE=.SIGMA.(E-E.sub.pred).sup.2
[0129] The SSE of a matrix of hypothetical K.sub.d and E.sub.max
values will be calculated on the computer as described. The
E.sub.max and K.sub.d of the protein pair expressed in HEK293 cells
will then be estimated based on the SEE.sub.min. The critical value
of the SSE for P=0.05 can be determined as described so the 95%
confidence intervals of E.sub.max and K.sub.d can be estimated. The
K.sub.d of different protein pairs will be compared to see if
different members of SUMO-specific peptidases and SUMO E3 ligases
favor interactions with different SUMO peptides.
[0130] FRET can be used to detect protein-protein interactions in
the SUMOylation network and to estimate the binding affinities of
different protein pairs in living cells. The FRET emission ratio,
which is the ratio of fluorescence intensity at the emission peak
of the acceptor and the donor under excitation of the donor, can
serve as judging criteria for the occurrence of FRET. Our
preliminary studies have shown that the interaction of SUMO1 and
Ubc9 results in a change of FRET ratio when they are tagged with
CyPet and YPet respectively. Changes in the FRET emission ratio are
expected to be seen for more protein pairs as interactions between
many proteins involved in the SUMOylation pathway have been proved.
Positive protein pairs which show an increase of FRET emission
ratio compared with the control group will be identified and the
disassociation constant K.sub.d of the protein pairs will be
estimated by subtracting cross-talk components from fluorescent
spectra followed by a computationally intense prediction of K.sub.d
and E.sub.max based on the least-square methods. Binding affinities
of SUMO-specific peptidases and SUMO E3 ligases (in our case PIASs)
will differ towards different members of SUMO peptides. The
comparison of their K.sub.d with different SUMO peptides will give
us information about their specificities in the SUMOylation and
deSUMOylation processes, which is still not fully understood.
[0131] The efficiency of FRET is highly dependent on the distance
between the donor and acceptor to the power of six. The Forster
distance of fluorescent proteins is around 40-50 .ANG., which is
comparable with the size of protein molecules. Therefore the FRET
efficiency of two fusion proteins in our assay is highly dependent
on the conformation of the fusion protein complexes. Conjugation of
CyPet/YPet onto different sites of target proteins such as the N-
or C-terminus will change the distance between two fluorescent
proteins. As a result, while the occurrence of FRET signal
indicates the interaction of two fusion proteins, lack of FRET
signal does not necessarily mean the tested fusion proteins do not
interact with each other. It is possible that even when two tested
proteins interact in living cells, the conjugated fluorescent
proteins are still separated by a long distance which makes the
FRET signal too small to be detectable under our experimental
settings.
[0132] It should be noticed that because the concentrations of the
donor and the acceptor are measured in units of fluorescence rather
than concentration units, estimated K.sub.d will be expressed in
units of fluorescence (RFU, Reference Unit) as well. The result is
dependent on the setting of the instrument such as the power of the
laser and the sensitivity of the sensor. In order to compare the
estimated K.sub.d between different protein pairs, FRET
measurements of transfected mammalian cells must be carried out
under the same experimental setting. While the estimated K.sub.d
does not have a concentration unit, the estimated K.sub.d can be
calibrated with the literature value from in vitro studies if it is
assumed that in vivo and in vitro binding affinities are
comparable. SUMO1-Ubc9 can be set as a standard.
[0133] In another embodiment, the disclosure provides FRET
constructs to screen small chemical inhibitors of protein-protein
interactions in the SUMOylation network. As the interaction of
CyPet/YPet-conjugated proteins recruits two fluorescent proteins
together and results in FRET, small chemical compounds disrupting
their interaction will separate the fluorescent proteins apart and
decrease the efficiency of FRET. HEK293 cell lines stably
expressing CyPet/YPet fusion proteins will be developed. Small
chemical libraries will be added onto the stable cell lines and
compounds decreasing the ratiometric FRET signal will be picked up
for further analysis.
[0134] 5.times.10.sup.4 per well HEK293 cells will be plated in
12-well tissue culture plate in 0.5 mL DMEM supplemented with 10%
FBS. After overnight incubation a pair of expression vectors
encoding CyPet and YPet fusion proteins respectively which shows an
increased FRET ratio will be used to transfect the cells with
FuGene6. 24 h after transfection, cells will be washed by PBS and
detached from the plate by trypsin. The suspended cells will then
be split into 15 cm tissue culture plate in 10 mL DMEM supplemented
with 10% fetal bovine serum. Hygromycin and geneticin (Invitrogen,
CA) will be added into the media the next day to a concentration of
150 .mu.g/mL and 750 .mu.g/mL, respectively. Cell culture medium
will be refreshed every 3-4 days to remove dead cells until the
living cells forms visible colonies in the plates. The stable cell
colonies will be transferred into 96-well plates and their
fluorescence emission at 475 nm and 530 nm will be determined under
excitation at 414 nm and 465 nm respectively. The colonies with
good expression of both proteins will be selected and serve in the
test group in the screening assay described below. Control cell
lines expressing different isoforms can be generated as the
specificity control group for the high through-put screening assay.
Taking cells expressing CyPet-SUMO and YPet-PIAS1 as an example,
the specificity control group will be stable cell lines expressing
CyPet-SUMO1 and YPet-PIAS3/x/y.
[0135] Optimization of the Assay and High-Throughput Screening of
Small Chemical Inhibitors:
[0136] Z factor has been widely used to assess the quality of
high-throughput screening assays. It is determined by the
variability in sample data as well as the dynamic range between the
high and low data populations. Z factor is defined as follows:
Z = 1 - ( 3 .sigma. s + 3 .sigma. c ) .mu. s - .mu. c
##EQU00014##
.mu..sub.s and .mu..sub.c are the means of the samples and control
populations, respectively. .sigma..sub.s and .sigma..sub.c are
designed as their standard deviation. Z factor is a dimensionless
factor between -1 and 1. It approaches 1 as the variability of the
data approaches 0 or the dynamic range of the assay approaches
infinity. To estimate the dynamic range and standard deviation of
positive hits, the stable cell lines will be transfected with
unconjugated acceptor proteins. Taking the HEK293 cells stably
expressing CyPet-SUMO1 and YPet-Ubc9 as an example, cells will be
transfected with different amount of unconjugated Ubc9. The
unconjugated Ubc9 will compete with fluorescent protein-tagged Ubc9
and decrease the FRET ratio of transfected cells. Transfected or
untransfected stable cell lines and mock transfected HEK293 cells
will be trypsinized, resuspended in PBS and aliquoted into 384-well
plates with various cell densities. The fluorescence intensities at
475 nm and 530 nm from each well will be determined by Flexstation
II.sup.384 under excitation at 414 nm and subtracted by those from
the mock transfected cells. Z factor will be determined for each
cell line at each cell density per well. The setting showing the
highest Z factor will be used for the screening assay.
[0137] For the high-throughput screening, cells in the test group
as well as mock transfected HEK293 cells will be aliquoted into
384-well plate based on the optimized setting and small chemical
compounds or vehicles will be added into each well to a final
concentration of 1 .mu.M. Compounds can be added to mock
transfected HEK293 cells as the background group. After incubation
at 37.degree. C. for 1 h, fluorescence intensities of each well
will be determined as described above and subtracted by those from
the background group. The FRET emission ratio (r) and FRET
efficiency (E) will then be calculated based on the algorithms
described above and compared with those from the untreated stably
transfected cells. The compounds showing a statistically
significant decrease of r or E will be picked up and can be further
tested in the specificity control group to determine the
specificity of their effects.
[0138] Cells stably expressing FRET protein pairs will be
generated. Z factor as a criterion of assay quality will be
determined for the best setting of the high-throughput screening
assay. Small chemical library will be applied to cells and the
fluorescence intensity from each well will be determined. The FRET
emission ratio and FRET efficiency of each well can be calculated
and compounds which decreases these two parameters will be picked
up and their specificity can be determined in the specificity
control group. At the conclusion of these proposed experiments,
potential small chemical inhibitors will be selected based on their
ability to disrupt the interaction between the tested protein pair,
which can be validated by the biological assays described
herein.
[0139] In the assay decrease of FRET signals can be achieved by not
only inhibitors disrupting protein-protein interactions, but also
fluorescence quenchers. Quenching of YPet fluorescence will result
in a decreased YPet sensitized emission regardless of the binding
status of the FRET protein pair. Therefore it is necessary for the
positive hits from the high-throughput screening to be further
characterized by fluorescence-independent techniques in order to
rule out the false positives.
[0140] The small chemical libraries used in the screening may
contain fluorescent compounds whose excitation spectrum overlaps
with that of CyPet. The direct emission from these fluorescent
compounds will interfere with the calculation of FRET efficiency
between the FRET protein pair. In the background control group of
our assay, compounds are added into mock transfected cells so both
the autofluorescence of the cells and the fluorescence of compounds
can be subtracted from the readings of test groups.
[0141] To develop secondary biochemical and biological assays to
validate and characterize potential small chemical inhibitors which
specifically disrupt the interaction between proteins involved in
the SUMOylation network. The inhibitors picked up from FRET-based
high-throughput screening maybe specific inhibitors disrupting
protein-protein interaction or simply fluorescence quenchers so it
will be necessary to develop secondary assays to validate their
activities. The methods of the disclosure include the use of
coimmunoprecipitation assays, yeast two-hybrid tests and in vitro
SUMOylation assays. In these assays, disruption of protein-protein
interaction by addition of specific inhibitors will lead to
decreased coimmunoprecipitation, changing of yeast phenotype or
inhibition of in vitro SUMOylation. In the following experiment
design session, the CyPet-SUMO1/YPet-PIAS1 pair will be used as an
example to demonstrate these assays in the validation of small
chemical inhibitors disrupting the interaction between SUMO1 and
PIAS1. The potential inhibitors of other protein pairs can be
analyzed following similar protocols.
[0142] To Validate Small Chemical Inhibitors Using SUMO1/PIAS1
Coimmunoprecipitation Assay:
[0143] HEK293 cells will be transfected with plasmids encoding
SUMO1 and PIAS1 using protocols described previously. After 48 h
incubation, cells will be lysed by RIPA lysis buffer and the
supernatant after centrifugation will used for the
immunoprecipitation assay. The potential chemical inhibitor
candidates will be added into the supernatant to different final
concentrations before SUMO1/PIAS1 complex is precipitated by
anti-SUMO1 antibodies. The amount of coimmunoprecipitated PIAS1
will be analyzed by western blots with anti-PIAS1 antibodies. The
intensity of PIAS1 on western blots will be quantified and plotted
against the final concentration of the inhibitor in the supernatant
to determine the IC.sub.50 of the inhibitor, at which the amount of
precipitated PIAS1 is decreased by 50%.
[0144] To Validate Small Chemical Inhibitors Using Yeast Two-Hybrid
Assay:
[0145] The ProQuest.TM. two-hybrid system (Invitrogen, CA) will be
used in the assay. In this system, the gene encoded in the bait
vector and the prey vector will be fused with the open reading
frame of GAL4 DNA binding domain and GAL4 activation domain
respectively. After the plasmids are transformed into the yeast
cells, bait and prey proteins will be expressed and their
interaction will recruit the GAL4 DNA binding domain and activation
domain together and drive the expression of auxotrophic markers
including HISS and URA3. Therefore the interaction of tested
proteins can be detected by the changes in the phenotype of
transformed yeast cells. In the experiment, SUMO1 and PIAS1 will be
cloned into the bait and prey expression vectors and transformed
into the Mav203 yeast strain following the protocol provided in the
kit. 5-fluoroorotic acid (5FOA) is a chemical compound which is
converted to a toxic compound in the presence of URA3. Therefore
the interaction of SUMO1 and PIAS1 will lead to the death of
transformed yeast cells when they are plated on medium containing
5FOA. The potential chemical inhibitor candidates will be added
onto the transformed yeasts to determine if they can disrupt the
interaction of SUMO1 and PIAS1 in yeast cells to rescue the
transformed yeasts on medium containing 5FOA. Alternatively,
because the expression of HISS and URA3 will allow cells to grow in
the absence of histidine and uracil, the small chemical inhibitors
can be added onto transformed yeast cells plated on medium lacking
histidine and uracil to determine if they can inhibit the growth of
transformed yeast cells.
[0146] To Validate Small Chemical Inhibitors Using In Vitro
SUMOylation Assay:
[0147] It is necessary to directly determine the effects of small
chemical inhibitors on the SUMOylation process. The heterodimeric
E1, Uba2 and Aos1, will be expressed and purified from bacteria.
Ubc9, SUMO1 and STAT1 can be purified from bacteria. Flag-tagged
PIAS1 protein will be obtained from mammalian cells. The assay will
be performed in a mixture containing purified proteins of
Uba2/Aos1, Ubc9, SUMO1, PIAS1 and STAT1 in an ATP regenerating
buffer (50 mM Tris-HCl at pH 7.6, 5 mM MgCl.sub.2, 2 mM ATP, 10 mM
creatine phosphate, 3.5 U/ml creatine kinase, and 0.6 U/ml
inorganic pyrophosphatase, 1.times. protease inhibitor cocktail) in
the presence or absence of various concentrations of inhibitors.
Reaction mixtures will be incubated at 37.degree. C. and analysed
by western blots with anti-SUMO1 or anti-STAT1 antibodies.
IC.sub.50 of the inhibitors can be determined when the secondary
antibody is labeled with fluorescence and the fluorescence is
quantified with fluorescence reader.
[0148] The major goal of the experiments is to establish a series
of secondary biological assays that can be used to confirm and
validate potential small chemical inhibitors disrupting
protein-protein interaction in the SUMOylation pathway. In the
first two assays two techniques commonly used to detect
protein-protein interaction were used to test if the potential
inhibitors can disrupt the interaction of their targets either in
vitro or in vivo. In the third assay the effects of potential
inhibitors on the SUMOylation process will be tested. At the
conclusion of these experiments small chemical inhibitors which can
disrupt the interaction of specific targets and manipulate the
activity of the SUMOylation pathway are identified. These
inhibitors will be subject to further analysis such as
function-structure studies.
[0149] In the yeast two-hybrid assay, both forward and reverse
two-hybrid assays are used. While in both cases addition of
inhibitors disrupts the interaction of bait and prey proteins and
inhibits the expression of HIS3 and URA3, in the forward two-hybrid
assay this results in the inhibition growth of transformed yeast
cells in the absence of histidine and uracil whereas in the reverse
two-hybrid assay this results in the growth of transformed yeast
cells in the presence of 5FOA. The reverse two-hybrid assay is
better than the forward assay in that it not only avoids the false
positive hits which kill yeast cells due to their cytotoxicity but
also rules out the chemicals functioning as a general inhibitors
for general transcriptional/translational machinery. However, the
positive hits generated from both assays may change the phenotypes
of transformed yeast cells by inhibiting the activities of HIS3 or
URA3 proteins. Another potential problem is that the inhibitors may
be able to get into the cytoplasm of mammalian cells but not yeast
cells so false negative results will be given for these inhibitors
in the yeast two-hybrid assays. Therefore the yeast two-hybrid
assay must be supplemented by other assays to validate the activity
and specificity of small chemical inhibitors identified as
above.
[0150] To validate the inhibitors disrupting SUMO-SENP interaction,
in vitro deSUMOylation assay are used. Myc-tagged SENP protein will
be expressed and purified in mammalian cells. Purified SENP
proteins will be mixed with in vitro SUMOylated STAT1. After
incubation at 37.degree. C., reaction product will be analyzed by
SDS-PAGE with anti-SUMO1 and anti-STAT1 antibodies. Various
concentrations of potential inhibitors will be added into the
reaction mixture and test if they can inhibit the deSUMOylation of
SUMOylated STAT1.
[0151] Synthesis of NBD Amino Acid and Fmoc-NBD Amino Acid
##STR00011##
[0152] Fmoc-NH-DAP-NBD-COOH.
[0153] To a stirred solution of sodium bicarbonate (0.154 g) and
N.alpha.-Fmoc, L-diamino propionic acid (0.5 g, 1.53 mmol) in 1:1
water and acetonitrile mixture (4 mL) was added
4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (0.367 g, 1.836 mmol). The
reaction mixture was allowed to stir overnight. Solvent was removed
using rotary evaporation, and the remaining crude was purified by
flash chromatograph on silica gel (CH.sub.2Cl.sub.2:MeOH=10:3) with
trance acetic acid to give product as brown solid (0.482 g, 0.985
mmol, 64.3%). .sup.1H NMR (400 MHz, DMSO, 25.degree. C.) .delta.
3.80 (bs, 2H), 4.15 (t, J=8.4 Hz, 1H), 4.28 (d, J=9.2 Hz, 2H), 4.37
(m, 1H), 6.48 (d, J=11.6 Hz, 1H), 7.24 (t, J=9.6 Hz, 2H), 7.35 (m,
2H), 7.60 (d, J=10.0 Hz, 2H), 7.63 (d, J=10.4 Hz, 1H), 7.85 (d,
J=10.0 Hz, 2H), 8.48 (d, J=10.4 Hz, 1H).
##STR00012##
[0154] Boc-NH-DAP-NBD-COOH.
[0155] To a stirred solution of sodium bicarbonate (0.049 g) and
N-Boc-L-2,3-diaminopropanoic acid (0.1 g) in a 1:1 water and
ethanol mixture was added 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole
(0.1 g) solution in 1:1 water and ethanol mixture. The reaction was
allowed to stir overnight. Solvent was removed using rotary
evaporation, and the remaining crude was dissolved in ethyl acetate
and the product was extracted using a saturated sodium bicarbonate
solution. The sodium bicarbonate fractions were combined and
neutralized with concentrated acetic acid until a pH of 5-6 was
achieved. The product
N-[(1,1-dimethylethoxy)carbonyl]-3-[(7-nitro-2,1,3-benzoxadiazol-4-yl)ami-
no]-L-alanine was extracted out of the aqueous solution using ethyl
acetate. The combined ethyl acetate phase were dried over sodium
sulfate, filtered, and the solvent removed by rotary evaporation.
.sup.1H NMR (300 MHz, DMSO, 25.degree. C.) .delta. 1.39 (s, 9H),
2.70 (m, (m 1H), 3.00 (dd, J=4.8 Hz, J=11.7 Hz, 1H), 3.15 (bs, 2H),
3.59 (m, 1H), 6.15 (m, 1H), 8.20 (bs, 1H).
[0156] NH-DAP-NBD-COOH.
[0157] Boc-NH-DAP-NBD-COOH was dissolved in methylene chloride and
TFA was dropped slowly. The resulted solution was stirred under rt
for 2.5 h. The solvent was removed under vacuum and afford the
result product
3-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-L-alanine .sup.1H NMR
(300 MHz, DMSO, 25.degree. C.) .delta. 4.01 (m, 2H), 4.30 (m, 1H),
6.63 (d, J=8.7 Hz, 1H), 8.70 (bs, 2H).
[0158] Synthesis of Fmoc-CUM Amino Acid for Peptide Synthesis
##STR00013##
Ethyl Magnesium Malonate (2)
[0159] To a stirred solution of monoethyl malonate 1 (1.65 g, 12.5
mmol) in THF (25 mL) was added the magnesium ethoxide (0.61 g, 6.25
mmol). The reaction mixture was allowed to stir at rt for 5 h
(until the solution become clear). The result solution was used for
next step without any treatment.
(2S)-2-benzyloxycarbonylamino-5-oxo-heptanedioic acid 1-benzyl
ester 7-ethyl ester (4)
[0160] Z-Glu-Obzl 3 (1.0 g, 2.7 mmol) was dissolved in dry THF (10
mL) at rt. Carbonyl diimidazole (0.48 g, 2.96 mmol) was added
slowly and the mixture was then stirred for another 2 h. After the
solution was cooled to 0.degree. C., ethyl magnesium malonate
solution 2 (4.7 mL, 1.2 mmol) was added, and the mixture was then
stirred at rt overnight. The product was extracted with ester, and
washed with 10% NaHCO.sub.3, water, and brine. After the solvent
was evaporated, the residue was purified by flash chromatography on
silica gel (Hexanes:EtOAc=1:1) and afford a white solid (0.9 g,
2.03 mmol, 75.2%). .sup.1H NMR (400 MHz, CDCl.sub.3, 25.degree. C.)
.delta. 1.23 (t, 3H), 1.90-2.00 (m, 1H), 2.10-2.30 (m, 1H),
2.50-2.70 (m, 2H), 3.36 (s, 2H), 4.16 (q, 2H), 4.30-4.50 (m, 1H),
5.10 (s, 2H), 5.12 (s, 2H) 5.36 (m, 1H), 7.25-7.40 (m, 10H).
[0161] L-(7-hydroxycoumarin-4-yl) ethylglycine (5) 4 (0.24 g, 0.543
mmol) was added slowly to resorcinol (0.3 g, 2.73 mmol) in
methanesulfonic acid (2 mL) at 0.degree. C. and stirred for 3 h at
rt. Ester (20 mL) was then added to the mixture and it was cooled
to -30.degree. C. The precipitate was washed with cold ether,
dissolved in water, filtered, and lyophilized to get 5. .sup.1H NMR
(400 MHz, DMSO, 25.degree. C.) .delta. 2.00-2.21 (m, 2H), 2.70-3.00
(m, 2H), 4.05 (m, 1H), 6.13 (s, 1H), 6.74 (d, 1H), 6.83 (dd, 1H),
7.62 (d, 1H), 8.33 (s, 3H).
L-Fmoc-amino-(7-hydroxycoumarin-4-yl) ethylglycine (6)
[0162] The coumaryl amino acid 5 (0.2 g, 0.557 mmol) dissolved in 4
mL 1:1 dioxane:water was treated at 0.degree. C. with NaHCO.sub.3
(0.187, 2.23 mmol). Then FmocCl (0.216, 0.836 mmol) was added at
0.degree. C. and stirred at rt for 3 h. The reaction mixture was
taken up in EtOAc, the organic extract was washed with water, 1N
HCl and brine, dried over anhydrous Na.sub.2SO.sub.4. After the
solvent was evaporated, the residue was purified by flash
chromatography on silica gel (Hexanes:EtOAc=1:1) and afford a pale
white solid (0.89 g, 0.183 mmol, 32.9%). .sup.1H NMR (400 MHz,
DMSO, 25.degree. C.) .delta. 1.90-2.10 (m, 2H), 2.70-2.90 (m, 2H),
4.02 (m, 1H), 4.10-4.40 (m, 3H), 4.70 (d, 2H), 6.06 (s, 1H), 6.72
(s, 1H), 6.80 (d, 1H), 7.20-7.50 (m, 4H), 7.60 (d, 1H), 7.80-8.00
(m, 4H).
[0163] Peptide Synthesis.
[0164] Synthesized peptide I
(Ala-NBD-Ala-Gln-Thr-Gly-Gly-Ala-CUM-Gly; SEQ ID NO:8) and II
(Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg-Tyr-Pro-Tyr-Asp-Tyr-Pro-Asp--
Try-Ala-NBD-Gln-Thr-Gly-Gly-CUM-Gly; SEQ ID NO:9) were carried out
by contract synthesis from C S BIO CO. (Menlo Park, Calif.
[0165] Protein expression and purification. SENP2 gene was
amplified using PCR and cloned in pET28(b) (Novagen. EMD Chemicals
Inc. San Diego, Calif.). Recombinant SENP2 was expressed in
bacteria strain B121(DE3) by 1 mM
isopropyl-.beta.-D-galactopyranoside (IPTG) at 37.degree. C. for 4
h and was purified by nickel affinity chromatography under standard
conditions.
[0166] Fluorescence Measurements.
[0167] Various concentrations of the peptide I were dissolved in
the buffer (25 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, 0.1% Tween 20,
modify pH at 8.0). Then the peptide solutions were transferred into
384 micro-well plate (Greiner Bio-one, New York, N.Y., US) at 30
.mu.l/well. Fluorescent intensity was measured with 340 nm
excitation wavelength (for coumarin) by FlexStation.TM. II.sup.384
(Molecular Device, Sunnyvale, Calif., US). Results are shown in
FIG. 13.
[0168] Peptide I and II at various concentrations were aliquoted
into 384 micro-well plate at 30 .mu.l/well. FRET assay was measured
by Flex SatationII.TM..sup.384 with the excitation wavelength of
340 nm. Result shows in FIG. 14.
[0169] Peptide I solution was aliquoted into 384 micro-well plate
at final concentration of 50 .mu.M of 30 .mu.l/well. Purified SENP2
was added to each well at final concentration of 15 .mu.M. After
the plate was gently agitated twice, the plate was sealed and
incubated at 37.degree. C. over night with aluminum foil covered.
Fluorescent intensity was measured by FlexStation II.TM. 384 the
excitation wavelength of 340 nm. Result shows in FIG. 15.
[0170] Peptide I solution was aliquoted into 384 micro-well plate
at final concentration of 25 .mu.M of 30 .mu.l/well. Purified SENP2
was added to each well at different concentrations of 1 uM and 15
uM. After the plate was gently agitated twice and then the plate
was sealed, the plate was covered with aluminum foil and incubated
at 37.degree. C. Fluorescent intensity was monitored by FlexStation
II.TM. .sup.384 at excitation wavelength of 340 nm at different
time point over the period of five hours. Result shows in FIG.
16.
[0171] As a novel application of fluorescent amino acid, this
combination of protein engineering and high-throughput chemical
screening will provide useful tools in SUMO studies but also
provide ideas to other areas of biological research in which
fluorescent amino acids and bioactive small chemicals can be used.
Sequence CWU 1
1
10184RNAArtificial SequencetRNA sequencemisc_feature(40)..(40)N is
a pseudouridinemisc_feature(60)..(60)N is a pseudouridine
1ggagggguag cgaaguggcu aaacgcggcg gacucuaaan ccgcucccuu uggguucggn
60cggcgaaucc gucccccucc acca 8428PRTArtificial sequenceCPP
consensus sequenceMISC_FEATURE(1)..(1)B is a basic amino
acidMISC_FEATURE(2)..(4)X is an alpha helix enhancing amino
acidMISC_FEATURE(5)..(5)B is a basic amino
acidMISC_FEATURE(6)..(7)X is an alpha helix enhancing amino
acidMISC_FEATURE(8)..(8)B is a basic amino acid 2Asx Xaa Xaa Xaa
Asx Xaa Xaa Asx 1 5 38PRTArtificial SequenceCPP consensus
sequenceMISC_FEATURE(1)..(1)B is a basic amino
acidMISC_FEATURE(2)..(3)X is an alpha helix enhancing amino
acidMISC_FEATURE(4)..(5)B is a basic amino
acidMISC_FEATURE(6)..(7)X is an alpha helix enhancing amino
acidMISC_FEATURE(8)..(8)B is a basic amino acid 3Asx Xaa Xaa Asx
Asx Xaa Xaa Asx 1 5 47PRTArtificial SequenceCPP peptide 4Lys Lys
Arg Pro Lys Pro Gly 1 5 511PRTArtificial SequenceCPP consensus
sequenceMISC_FEATURE(1)..(2)X is any alpha helical enhancing amino
acidMISC_FEATURE(4)..(4)X is any alpha helical enhancing amino
acidMISC_FEATURE(5)..(5)X is any alpha helical enhancing amino acid
or ProlineMISC_FEATURE(6)..(6)X is any alpha helical enhancing
amino acid or a basic amino acidMISC_FEATURE(7)..(7)X is a basic
amino acidMISC_FEATURE(8)..(8)X is any alpha helical enhancing
amino acid or prolineMISC_FEATURE(9)..(9)X is any alpha helical
enhancing amino acidMISC_FEATURE(10)..(10)X is a basic amino
acidMISC_FEATURE(11)..(11)X is any alpha helical enhancing amino
acid or a basic amino acid 5Xaa Xaa Arg Xaa Xaa Xaa Xaa Xaa Xaa Xaa
Xaa 1 5 10 65PRTArtificial SequenceCPP consensus
sequenceMISC_FEATURE(2)..(2)X is R or KMISC_FEATURE(4)..(4)X is any
amino acidMISC_FEATURE(5)..(5)X is R or K 6Lys Xaa Arg Xaa Xaa 1 5
79PRTArtificial SequenceCPP peptide 7Arg Lys Lys Arg Arg Gln Arg
Arg Arg 1 5 810PRTArtificial SequenceLabeled
peptideMISC_FEATURE(2)..(2)X is a NBD amino
acidMISC_FEATURE(9)..(9)X is a CUM labeled amino acid 8Ala Xaa Ala
Gln Thr Gly Gly Ala Xaa Gly 1 5 10 927PRTArtificial SequenceLabeled
peptideMISC_FEATURE(21)..(21)X is an NBD amino
acidMISC_FEATURE(26)..(26)X is CUM labeled amino acid 9Tyr Gly Arg
Lys Lys Arg Arg Gln Arg Arg Arg Tyr Pro Tyr Asp Tyr 1 5 10 15 Pro
Asp Tyr Ala Xaa Gln Thr Gly Gly Xaa Gly 20 25 104PRTArtificial
SequenceLinking peptide 10Gln Thr Gly Gly 1
* * * * *