Claims
- 1. An isolated isomerase comprising at least twelve α-carbon atoms having the three-dimensional structure substantially equivalent to the three-dimensional structure defined by residues 36, 37, 38, 47, 48, 50, 106, 109, 110, 113, 190 and 191 of Table 1.
- 2. The isolated isomerase of claim 1, further comprising α-carbon atoms having the three-dimensional structure substantially equivalent to the three-dimensional structure defined by residues 49, 97, 101, 112, 150, 152, and 200 of Table 1.
- 3. The isolate isomerase of claim 1, wherein the amino acid located at position 36 is Methionine, Lysine, Alanine, Histidine or Glutamine.
- 4. The isolated isomerase of claim 1, wherein the amino acid located at position 38 is Leucine or Alanine.
- 5. The isolated isomerase of claim 1, wherein the amino acid located at position 48 is Threonine, Alanine or Serine.
- 6. The isolated isomerase of claim 1, wherein the amino acid located at position 106 is Tyrosine, Phenylalanine or Serine.
- 7. The isolated isomerase of claim 1, wherein the amino acid located at position 109 is Lysine or Methionine.
- 8. The isolated isomerase of claim 1, wherein the amino acid located at position 110 is Valine, Alanine or Glycine.
- 9. The isolated isomerase of claim 1, wherein the amino acid located at position 113 is Asparagine or Alanine.
- 10. The isolated isomerase of claim 1, wherein the amino acid located at position 190 is Threonine or Alanine.
- 11. The isolated isomerase of claim 1, wherein the amino acid at position 190 is Serine and the amino acid at position 191 is Isoleucine.
- 12. The isolated isomerase of claim 1, wherein the isomerase has atomic coordinates as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP or Table 1.
- 13. A nucleic acid encoding the isomerase of claim 1.
- 14. A method of predicting the activity and/or substrate specificity of a putative isomerase, said method comprising:
comparing the representation of a known isomerase and the representation of a putative isomerase, wherein differences between the two representations are predictive of isomerase activity and/or substrate specificity.
- 15. The method of claim 14, wherein the known isomerase is chalcone isomerase.
- 16. The method of claim 15, wherein the, known chalcone isomerase has strucutral coordinants as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP or Table 1.
- 17. The method of claim 14, wherein the putative isomerase is a mutant of a known isomerase.
- 18. A crystalline form of the isomerase of claim 1.
- 19. The crystalline isomerase of claim 18, wherein the isomerase is a chalcone isomerase.
- 20. A crystalline complex comprising chalcone isomerase and a chalcone isomerase product.
- 21. The crystalline complex of claim 20, wherein the chalcone isomerase is native chalcone isomerase.
- 22. The crystalline complex of claim 20, wherein the chalcone isomerase is a non-native chalcone isomerase.
- 23. The crystalline complex of claim 20, wherein the chalcone isomerase product is selected from the group consisting of naringenin, 5-deoxyflavanone, 5,4′-dideoxyflavanone, 7,4′-dihydroxyflavanone, 7-hydroxyflavanone, and 4′-dihydroxyflavanone.
- 24. The crystalline complex of claim 20, wherein the complex has atomic coordinates as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP or Table 1.
- 25. A method of identifying a potential substrate of an isomerase, said method comprising:
(a) defining an active site of said isomerase based on a plurality of atomic coordinates of said isomerase; (b) identifying a potential substrate that fits the active site of (a); and (c) contacting the isomerase with the potential substrate and determining its activity thereon.
- 26. The method of claim 25, wherein the isomerase is chalcone isomerase.
- 27. The method of claim 25, wherein the isomerase is a mutant of a known isomerase.
- 28. The method of claim 27, wherein the known isomerase is chalcone isomerase.
- 29. The method of claim 25, wherein the plurality of atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, Table 1, or a subset or portion thereof.
- 30. A method of identifying a potential inhibitor of an isomerase, said method comprising:
(a) contacting a potential compound that fits an active site defined based on a plurality of atomic coordinates of said isomerase; and (b) determining the ability of said compound to inhibit the activity of said isomerase.
- 31. The method of claim 30, wherein the isomerase is chalcone isomerase.
- 32. The method of claim 30, wherein the isomerase is a mutant of a known isomerase.
- 33. The method of claim 32, wherein the mutant isomerase is a mutant of chalcone isomerase.
- 34. The method of claim 30, wherein the plurality of atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, Table 1, or a subset or portion thereof.
- 35. A computer program on a computer readable medium, said computer program comprising instructions to cause a computer to:
define an isomerase or fragment thereof based on a plurality of atomic coordinates of the isomerase.
- 36. The computer program of claim 35, wherein the plurality of atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, Table 1, or a subset or portion thereof.
- 37. A computer for producing a three-dimensional representation of a molecule or molecular complex or a homologue of said molecule or molecular complex, wherein said molecule or molecular complex or a homologue of said molecule or molecular complex comprises an active site defined by atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, or Table 1, wherein said computer comprises:
(i) a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, or Table 1; (ii) a working memory for storing instructions for processing said computer-readable data; (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium for processing said computer-machine readable data into said three-dimensional representation; and (iv) a display coupled to said central-processing unit for displaying said three-dimensional representation.
- 38. A computer for determining at least a portion of the atomic coordinates corresponding to X-ray diffraction data obtained from a molecule or molecular complex or a homologue of said molecule or molecular complex, wherein said molecule or molecular complex or a homologue of said molecule or molecular complex comprises an active site defined by atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, or Table 1, wherein said computer comprises:
(i) a computer-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises at least a portion of the atomic coordinates are as set forth in PDB Accession Nos: 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, Table 1; (ii) a working memory for storing instructions for processing said computer-readable data; (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium of (i) and (ii) for performing a Fourier transform of the machine readable data of (i) and for processing said computer-readable data of (ii) into structure coordinates; and (iv) a display coupled to said central-processing unit for displaying said structure coordinates of said molecule or molecular complex.
- 39. A method of screening compounds to determine whether they are isomerase substrates, said method comprising:
a) determining the points of interaction between an isomerase and a substrate or product therefor; b) selecting compound(s) having similar interaction with said isomerase; and c) testing the selected compound for the ability to be converted by said isomerase.
- 40. A method of screening compounds to determine whether they are isomerase substrates, said method comprising:
a) selecting compound(s) having points of interaction with said isomerase, wherein similar points of interaction have been determined between said isomerase and a substrate or product therefor; and b) testing the selected compound for the ability to be converted by said isomerase.
- 41. A method of screening compounds to determine whether they are isomerase substrates, said method comprising:
testing a compound for the ability to be converted by said isomerase, wherein said compound has been selected as having points of interaction with said isomerase, and wherein similar points of interaction have been determined between said isomerase and a substrate or product therefor.
- 42. The compound identified by the method of claim 39.
- 43. A composition comprising a compound identified by the method of claim 39 and an acceptable carrier therefor.
- 44. A method for stimulating the activity of an isomerase, said method comprising contacting said isomerase with an effective amount of a compound identified by the method of claim 39.
- 45. A method for screening for compounds that inhibit an isomerase, said method comprising:
a) determining the points of interaction between an isomerase and a substrate or product therefor; b) selecting compound(s) having similar interaction with said isomerase; and c) testing the selected compound for the ability to inhibit the activity of said isomerase.
- 46. A method for screening for compounds that inhibit an isomerase, said method comprising:
a) selecting compound(s) having points of interaction with an isomerase, wherein similar points of interaction have been determined between said isomerase and a substrate or product therefor; and b) testing the selected compound for the ability to inhibit the activity of said isomerase.
- 47. A method for screening for compounds that inhibit an isomerase, said method comprising:
testing a compound for the ability to inhibit the activity of said isomerase, wherein said compound has been selected as having points of interaction with said isomerase, and wherein similar points of interaction have been determined between said isomerase and a substrate or product therefor.
- 48. A compound identified by the method of claim 45.
- 49. A composition comprising a compound identified by the method of claim 45 and an acceptable carrier therefor.
- 50. A method for inhibiting the activity of an isomerase, said method comprising contacting said isomerase with an effective amount of a compound identified by the method of claim 45.
RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Application No. 60/229,277, filed Aug. 30, 2000, which is hereby incorporated by reference herein in its entirety.
ACKNOWLEDGMENT
[0002] This invention was made with United States Government support under Grant No. MCB-9982586, awarded by the National Science Foundation. The Government has certain rights in the invention.
PCT Information
Filing Document |
Filing Date |
Country |
Kind |
PCT/US01/27027 |
8/29/2001 |
WO |
|