Methods and kits using a molecular interaction between a Smurf-1 WW domain and LIM mineralization protein isoforms
The instant application provides kits and methods for identifying agents which induce or inhibit the osteogenic effect of LMP or BMP proteins. The kits are directed to methods which measure either an amount of a complex between a Smurf protein or a fragment thereof and an LMP protein or a fragment thereof. Alternatively, the kits are directed to methods of measuring an amount of the ubiquitinated Smad protein or a fragment thereof.
1. A method of identifying an agent affecting a binding between an LMP protein and a Smurf1 protein comprising:
providing a first composition comprising:
a first amino acid sequence comprising the amino acid sequence of SEQ ID NO: 41;
a second amino acid sequence comprising an amino acid sequence at least 90% identical to SEQ ID NO: 2 and capable of binding the amino acid sequence of SEQ ID NO: 41; and
the agent; and
measuring an amount of a complex formed between the first amino acid sequence and the second amino acid sequence in the first composition; and
comparing the amount of the complex in the first composition with an amount of a complex formed between a third amino acid sequence and a fourth amino acid sequence in a second composition, wherein:
said second composition does not include the agent;
the third amino acid sequence comprises the amino acid sequence of SEQ ID NO: 41: and
the fourth amino acid sequence comprises an amino acid sequence at least 90% identical to SEQ ID NO: 2 and capable of binding the amino acid sequence of SEQ ID NO: 41, and wherein further each of said second and said fourth amino acid sequences comprises:
leucine at a position corresponding to position 3 of SEQ ID NO: 2;
proline at a position corresponding to position 4 of SEQ ID NO: 2;
tryptophan at a position corresponding to position 7 of SEQ ID NO: 2;
glutamic acid at a position corresponding to position 8 of SEQ ID NO: 2;
arginine, lysine or alanine at a position corresponding to position 10 of SEQ ID NO: 2;
tyrosine, phenylalanine or isoleucine at a position corresponding to position 18 of SEQ ID NO: 2;
phenylalanine or isoleucine at a position corresponding to position 19 of SEQ ID NO: 2;
valine or isoleucine at a position corresponding to position 20 of SEQ ID NO: 2;
asparagine or aspartic acid at a position corresponding to position 21 of SEQ ID NO: 2;
histidine at a position corresponding to position 22 of SEQ ID NO: 2;
asparagine, valine, proline or serine at a position corresponding to position 23 of SEQ ID NO:2;
arginine or lysine at a position corresponding to position 25 of SEQ ID NO: 2;
serine or threonine at a position corresponding to position 27 of SEQ ID NO: 2;
glutamine at a position corresponding to position 28 of SEQ ID NO: 2;
aspartic acid at a position corresponding to position 31 of SEQ ID NO: 2;
proline at a position corresponding to position 32 of SEQ ID NO: 2; and
arginine at a position corresponding to position 33 of SEQ ID NO: 2.
2. The method of claim 1 , wherein each of said second and fourth sequence comprises SEQ ID NO: 2 and is capable of binding the amino acid sequence of SEQ ID NO: 41.
3. The method of claim 1 , wherein
an increased amount of the complex in the first composition indicates that the agent induces binding between the first amino acid sequence and the second amino acid sequence; and
a decreased amount of the complex in the first composition indicates that the agent inhibits binding between the first amino acid sequence and the second amino acid sequence.
4. The method of claim 1 , wherein
an increased amount of the complex in the first composition indicates that the agent inhibits ubiquitination of a Smad protein by Smurf1; and
a decreased amount of the complex in the first composition indicates that the agent induces ubiquitination of a Smad protein by Smurf1.
5. The method of claim 4 , wherein the Smad protein is selected from the group consisting of a Smad1 protein, a Smad5 protein, and a Smad6 protein.
6. The method of claim 1 , wherein
an increased amount of the complex in the first composition indicates that the agent induces an osteogenic effect of an LMP protein or a fragment thereof; and
a decreased amount of the complex in the first composition indicates that the agent inhibits an osteogenic effect of an LMP protein or a fragment thereof.
7. The method of claim 6 , wherein the LMP protein or the fragment thereof is selected from the group consisting of LMP-1, corresponding to SEQ ID NO: 53, LMP-3 corresponding to SEQ ID NO: 54, and LMP-1s corresponding to SEQ ID NO: 55.
8. The method of claim 2 , wherein
the first amino acid sequence is identical to the third amino acid sequence, or
the second amino acid sequence is identical to the fourth amino acid sequence, or
the first amino acid sequence is identical to the third amino acid sequence and the second amino acid sequence is identical to the fourth amino acid sequence.
9. The method of claim 1 , wherein the SEQ ID NO: 41 is incorporated within SEQ ID NO: 4.
10. The method of claim 1 , wherein the amino acid sequence at least 90% identical to SEQ ID NO. 2 and capable of binding the amino acid sequence of SEQ ID NO: 41 is 100% identical to SEQ ID NO. 2.
11. The method of claim 1 , wherein the amino acid sequence at least 90% identical to SEQ ID NO: 2 comprises:
arginine at a position corresponding to position 10 of SEQ ID NO: 2;
tyrosine at a position corresponding to position 18 of SEQ ID NO: 2;
arginine at a position corresponding to position 25 of SEQ ID NO: 2;
threonine at a position corresponding to position 27 of SEQ ID NO 2.
12. The method of claim 1 , wherein the first composition and the second composition are cell-free systems.