초록 ▼

The present invention relates to the three dimensional solution structure of the N-terminal domain of TNFR-1 associated death domain protein ("N-TRADD"), as well as the identification and characterization of a C-TRAF2 binding active site of N-TRADD. Also provided for by the present invention are met

The present invention relates to the three dimensional solution structure of the N-terminal domain of TNFR-1 associated death domain protein ("N-TRADD"), as well as the identification and characterization of a C-TRAF2 binding active site of N-TRADD. Also provided for by the present invention are methods of utilizing the three dimensional structures for the design and selection of potent and selective inhibitors of TNF signaling pathways.

대표청구항 ▼

What is claimed is: 1. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: providing a solution comprising N-TRADD; displaying a three-dimensional model of an active site of N-TRADD, wherein the active s

What is claimed is: 1. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: providing a solution comprising N-TRADD; displaying a three-dimensional model of an active site of N-TRADD, wherein the active site of N-TRADD comprises an N-terminal domain of TRADD that interacts with C-TRAF2 and wherein the three dimensional structure of the active site comprises the relative structural coordinates of amino acid residues Y16, L17, F18, V58, L59, K63, I64, H65, D68, Q70, I72, V73, Q74, L75, C78, L118, G121, A122, R124, L125, D149, E150, and L152 according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of the amino acids of the active site of not more than 1.5Å; using the three-dimensional structure of the active site of N-TRADD to design an agent that interacts with the active site of N-TRADD; and obtaining or synthesizing the agent. 2. The method of claim 1, wherein the three-dimensional structure of the active site of N-TRADD is a solution structure of the active site of N-TRADD. 3. The method of claim 1, wherein the three-dimensional structure of the active site of N-TRADD is obtained from NMR data. 4. The method of claim 1, wherein the design of the agent comprises using molecular modeling. 5. The method of claim 1, further comprising contacting the agent with N-TRADD and determining the effect of the agent on N-TRADD activity. 6. The method of claim 5, wherein the agent is an inhibitor of the active site of N-TRADD. 7. The method of claim 1, wherein the three dimensional structure of the active site of N-TRADD comprises the relative structural coordinates of the amino acid residues of N-TRADD according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å. 8. The method of claim 7, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 1.0Å. 9. The method of claim 8, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 10. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: displaying a three-dimensional model of an active site of N-TRADD, wherein the active site of N-TRADD comprises an N-terminal domain of TRADD that interacts with C-TRAF2 and wherein the three dimensional model of the active site of N-TRADD comprises the relative structural coordinates of amino acid residues Y16, L17, F18, V58, L59, K63, I64, H65, D68, Q70, I72, V73, Q74, L75, C78, L118, G121, A122, R124, L125, E150, and L152 according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å; using the three-dimensional structure of the active site of N-TRADD to design an agent that interacts with the active site of N-TRADD;and obtaining or synthesizing the agent. 11. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: providing a solution comprising N-TRADD; using a three-dimensional structure of an active site of N-TRADD to design an agent that interacts with the active site of N-TRADD, wherein: the active site of N-TRADD comprises the relative structural coordinates of amino acid residues Y16, L17, F18, V58, L59, K63, I64, H65, D68, Q70, I72, V73, Q74, L75, C78, L118, G121, A122, R124, L125, E150, and L152 according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å; and obtaining the agent. 12. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: providing a solution comprising N-TRADD; using a three-dimensional structure of an active site of N-TRADD to design an agent that interacts with the active site of N-TRADD, wherein: the active site of N-TRADD comprises the relative structural coordinates of amino acid residues Y16, L17, F18, V58, L59, K63, I64, H65, D68, Q70, I72, V73, Q74, L75, C78, L118, G121, A122, R124, L125, E150, and L152 according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5 Å; obtaining the agent; and interacting the agent with the active site of N-TRADD to determine the effect the agent has on the activity of the active site of N-TRADD. 13. The method of claim 1 or 10, wherein the design of the agent comprises using computer fitting analysis. 14. A method for identifying an agent that interacts with N-terminal domain of TNFR-1 associated death domain protein (N-TRADD), the method comprising: displaying a three-dimensional structure of an active site of N-TRADD, wherein the active site of N-TRADD comprises the relative structural coordinates of amino acid residues Y16, L17, F18, V58, L59, K63, I64, H65, D68, Q70, I72, V73, Q74, L75, C78, L118, G121, A122, R124, L125, E150, and L152 according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å; evaluating the ability of the agent to associate with the three-dimensional structure of the active site of N-TRADD; and designing the agent and displaying graphical representing of the designed agent; wherein the agent is designed de novo or using known inhibitors of N-TRADD. 15. The method of claim 10 or 14, wherein the design of the agent comprises using molecular modeling. 16. The method of claim 1, further comprising storing the three-dimensional structure of the active site of N-TRADD in a machine readable storage medium. 17. The method of claim 1, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 1.0Å. 18. The method of claim 1, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 19. The method of claim 14, wherein the root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.0Å. 20. The method of claim 11, wherein the three dimensional structure of the active site of N-TRADD comprises the relative structural coordinates of the amino acid residues of N-TRADD according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å. 21. The method of claim 12, wherein the three dimensional structure of the active site of N-TRADD comprises the relative structural coordinates of the amino acid residues of N-TRADD according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å. 22. The method of claim 14, wherein the three dimensional structure of the active site of N-TRADD comprises the relative structural coordinates of the amino acid residues of N-TRADD according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å. 23. The method of claim 1, wherein N-TRADD comprises amino acid residues 1-169 of TRADD as shown in FIG. 1, or one or more conservative substitutions thereof. 24. The method of claim 10, further comprising storing the three-dimensional structure of the active site of N-TRADD in a machine readable storage medium. 25. The method of claim 24, wherein the agent is generated de novo or using known inhibitors of N-TRADD. 26. The method of claim 10, wherein the three-dimensional structure of the active site of N-TRADD is a solution structure of the active site of N-TRADD. 27. The method of claim 10, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 1.0Å. 28. The method of claim 10, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 29. The method of claim 10, further comprising contacting the agent with N-TRADD and determining the effect of the agent on N-TRADD activity. 30. The method of claim 10, wherein N-TRADD comprises amino acid residues 1-169 of TRADD as shown in FIG. 1, or one or more conservative substitutions thereof. 31. The method of claim 11, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 1.0Å. 32. The method of claim 11, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 33. The method of claim 11, further comprising contacting the agent with N-TRADD and determining the effect of the agent on N-TRADD activity. 34. The method of claim 11, wherein N-TRADD comprises amino acid residues 1-169 of TRADD as shown in FIG. 1, or one or more conservative substitutions thereof. 35. The method of claim 12, wherein the agent is designed de novo or using known inhibitors of N-TRADD. 36. The method of claim 12, wherein N-TRADD comprises amino acid residues 1-169 of TRADD as shown in FIG. 1, or one or more conservative substitutions thereof. 37. The method of claim 12, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 1.0Å. 38. The method of claim 12, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 39. The method of claim 14, further comprising storing the three-dimensional structure of the active site of N-TRADD in a machine readable storage medium. 40. The method of claim 14, further comprising contacting the agent with N-TRADD and determining the effect of the agent on N-TRADD activity. 41. The method of claim 14, further comprising obtaining or synthesizing the agent. 42. The method of claim 14, wherein the three-dimensional structure of the active site of N-TRADD is obtained from NMR data. 43. The method of claim 40, wherein the agent is an inhibitor of the active site of N-TRADD. 44. The method of claim 14, wherein N-TRADD comprises amino acid residues 1-169 of TRADD as shown in FIG. 1, or one or more conservative substitutions. 45. The method of claim 14, wherein the design of the agent comprises using molecular modeling or computer fitting analysis. 46. The method of claim 14, wherein the root mean square deviation from the conserved backbone atoms of said amino acids is not more than 0.5Å. 47. The method of claim 10, wherein the three dimensional structure of the active site of N-TRADD further comprises the relative structural coordinates according to FIG. 2, �� a root mean square deviation from the conserved backbone atoms of said amino acids of not more than 1.5Å.