Methods and compositions for targeting polyubiquitin
Anti-K63-linked polyubiquitin monoclonal antibodies, and methods for using the antibodies, are provided.
1. An isolated antibody or antigen-binding fragment thereof that specifically binds to K63-linked polyubiquitin, comprising the HVR-H1 sequence of SEQ ID NO: 5, the HVR-H2 sequence of SEQ ID NO: 63, the HVR-H3 sequence of SEQ ID NO: 6, the HVR-L1 sequence of SEQ ID NO: 3, the HVR-L2 sequence of SEQ ID NO: 11, and the HVR-L3 sequence of SEQ ID NO: 4.
2. The isolated antibody or antigen binding fragment thereof of claim 1 , which is a mouse, chimeric, or humanized antibody or antigen binding fragment thereof.
3. The isolated antibody or antigen binding fragment thereof of claim 1 , which has an affinity (K d ) for K63-linked polyubiquitin of less than or equal to 10 nM.
4. The isolated antibody or antigen binding fragment thereof of claim 1 , wherein the antibody or antigen binding fragment thereof does not specifically bind to K48-linked polyubiquitin or monoubiquitin.
5. The isolated antibody or antigen-binding fragment thereof of claim 1 , wherein the antibody or antigen-binding fragment has at least one property selected from inhibiting degradation of the K63-linked polyubiquitinated protein, modulating at least one polyubiquitin-mediated signaling pathway, inhibiting at least one polyubiquitin-mediated signaling pathway, and stimulating at least one polyubiquitin-mediated signaling pathway.
6. A composition comprising the antibody or antigen-binding fragment thereof of claim 1 and a pharmaceutically acceptable carrier.
7. An isolated monoclonal antibody or antigen-binding fragment thereof that binds to the same antigenic determinant on K63-linked polyubiquitin as the antibody or antigen-binding fragment of claim 1 .
8. The isolated monoclonal antibody or antigen binding fragment thereof of claim 7 , which is a mouse, chimeric, human, or humanized antibody or antigen binding fragment thereof.
9. The isolated monoclonal antibody or antigen binding fragment thereof of claim 7 , wherein the antibody or antigen binding fragment thereof does not specifically bind to K48-linked poly ubiquitin or monoubiquitin.
10. The isolated monoclonal antibody or antigen-binding fragment thereof of claim 7 , wherein the antibody or antigen-binding fragment has at least one property selected from inhibiting degradation of the K63-linked polyubiquitinated protein, modulating at least one polyubiquitin-mediated signaling pathway, inhibiting at least one polyubiquitin-mediated signaling pathway, and stimulating at least one polyubiquitin-mediated signaling pathway.
11. A composition comprising the monoclonal antibody or antigen-binding fragment thereof of claim 7 and a pharmaceutically acceptable carrier.
12. An isolated monoclonal antibody or antigen-binding fragment thereof that competes with the antibody of claim 1 for binding to K63-linked polyubiquitin.
13. The isolated monoclonal antibody or antigen binding fragment thereof of claim 12 , which is a mouse, chimeric, human, or humanized antibody or antigen binding fragment thereof.
14. The isolated monoclonal antibody or antigen binding fragment thereof of claim 12 , wherein the antibody or antigen binding fragment thereof does not specifically bind to monoubiquitin.
15. The isolated monoclonal antibody or antigen-binding fragment thereof of claim 12 , wherein the antibody or antigen-binding fragment has at least one property selected from inhibiting degradation of the K63-linked polyubiquitinated protein, modulating at least one polyubiquitin-mediated signaling pathway, inhibiting at least one polyubiquitin-mediated signaling pathway, and stimulating at least one polyubiquitin-mediated signaling pathway.
16. A composition comprising the monoclonal antibody or antigen-binding fragment thereof of claim 12 and a pharmaceutically acceptable carrier.
17. A method of identifying the presence of K63-linked polyubiquitin or a K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one antibody or antigen-binding fragment thereof of claim 1 .
18. A method of identifying the presence of K63-linked polyubiquitin or a K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one monoclonal antibody or antigen-binding fragment thereof of claim 9 .
19. A method of identifying the presence of K63-linked polyubiquitin or a K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one monoclonal antibody or antigen-binding fragment thereof of claim 14 .
20. A method of separating K63-linked polyubiquitinated protein from non-K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one antibody or antigen-binding fragment of claim 1 .
21. A method of separating K63-linked polyubiquitinated protein from non-K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one monoclonal antibody or antigen-binding fragment of claim 9 .
22. A method of separating K63-linked polyubiquitinated protein from non-K63-linked polyubiquitinated protein in a sample, comprising contacting the sample with at least one monoclonal antibody or antigen-binding fragment of claim 14 .