In vivo protein screen based on enzyme-assisted chemically induced dimerization ("CID")
First Claim
1. A method for identifying which protein from a pool of candidate proteins catalyzes in a cell a bond forming reaction between a first substrate and a second substrate, comprising:
- (a) providing a dimeric small molecule which comprises a known moiety that binds a known receptor domain covalently linked with a moiety that contains the first substrate;
(b) introducing the dimeric molecule into a cell which comprises i) a first fusion protein comprising the known receptor domain, ii) a second fusion protein comprising the second substrate, iii) a protein from the pool of candidate proteins, and iv) a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the dimeric molecule to bind to the first fusion protein and to enzymatically form a bond with the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the protein that catalyzes the bond formation reaction in the cell between the first substrate and the second substrate.
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Abstract
A method for identifying which protein from a pool of candidate proteins catalyzes in a cell a bond forming reaction between a first substrate and a second substrate, comprising:
(a) providing a dimeric small molecule which comprises a known moiety that binds a known receptor domain covalently linked with a moiety that contains the first substrate;
(b) introducing the dimeric molecule into a cell which comprises
i) a first fusion protein comprising the known receptor domain,
ii) a second fusion protein comprising the second substrate,
iii) a protein from the pool of candidate proteins, and
iv) a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the dimeric molecule to bind to the first fusion protein and to enzymatically form a bond with the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the protein that catalyzes the bond formation reaction in the cell between the first substrate and the second substrate. The method is also adapted to identify which substrate from a pool of candidate substrates is selected in a cell by a known enzyme for a bond forming reaction between the substrate and a known amino acid. Also, cells, compounds and kits for carrying out the methods.
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Citations
83 Claims
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1. A method for identifying which protein from a pool of candidate proteins catalyzes in a cell a bond forming reaction between a first substrate and a second substrate, comprising:
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(a) providing a dimeric small molecule which comprises a known moiety that binds a known receptor domain covalently linked with a moiety that contains the first substrate;
(b) introducing the dimeric molecule into a cell which comprises i) a first fusion protein comprising the known receptor domain, ii) a second fusion protein comprising the second substrate, iii) a protein from the pool of candidate proteins, and iv) a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the dimeric molecule to bind to the first fusion protein and to enzymatically form a bond with the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the protein that catalyzes the bond formation reaction in the cell between the first substrate and the second substrate. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32)
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33. A method for identifying which substrate from a pool of candidate substrates is selected in a cell by a known enzyme for a bond forming reaction between the substrate and a known amino acid, comprising:
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(a) providing a dimeric small molecule which comprises the substrate covalently linked to a moiety known to bind a receptor domain;
(b) introducing the dimeric molecule into a cell which comprises i) a first fusion protein comprising the receptor domain, ii) a second fusion protein comprising the known amino acid, iii) the known enzyme, and iv) a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the dimeric molecule to bind to the first fusion protein and to enzymatically form a bond with the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the substrate selected by the known enzyme in the cell for the bond forming reaction between the substrate and the known amino acid. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50)
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51. A transgenic cell comprising
(a) a dimeric small molecule which comprises a moiety known to bind a receptor domain covalently linked to a first substrate of an enzyme; -
(b) nucleotide sequences which upon transcription encode i) the enzyme, ii) a first fusion protein comprising the receptor domain, and ii) a second fusion protein comprising a second substrate of the enzyme; and
(c) a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein. - View Dependent Claims (52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78)
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79. A kit for detecting bond formation by an enzyme between a first substrate and a second substrate in a cell, comprising
(a) a host cell containing a reporter gene that is expressed only when bound to a DNA-binding domain and when in the proximity of a transcription activation domain; -
(b) a first vector containing a promoter that functions in the host cell and a DNA encoding a DNA-binding domain;
(c) a second vector containing a promoter that functions in the host cell and a DNA encoding a transcription activation domain;
(d) a third vector containing a promoter that functions in the host cell;
(e) a dimeric small molecule which comprises a moiety known to bind a receptor domain and a moiety containing the first substrate of the enzyme;
(f) a means for inserting into the first vector or the second vector a DNA encoding a receptor domain in such a manner that the receptor domain and the DNA-binding domain are expressed as a fusion protein;
(g) a means for inserting into the first vector or the second vector a DNA encoding a protein containing the second substrate of the enzyme in such a manner that the protein and the transcription activation domain are expressed as a fusion protein;
(h) a means for inserting into the third vector a DNA encoding the enzyme; and
(h) a means for transfecting the host cell with the first vector, the second vector, and the third vector, wherein bond formation by the enzyme between the first substrate and the second substrate results in a measurably greater expression of the reporter gene then in the absence of bond formation by the enzyme.
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- 80. A small molecule compound having the structure:
Specification