A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains

Journal of the American Chemical Society

Volumn 127, Issue 40, 2005, Pages 14072-14079

  Niv, Masha Y ^a   Weinstein, Harel ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CONFORMATIONS; INFORMATION ANALYSIS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MUTAGENESIS; NETWORK PROTOCOLS; SIMULATED ANNEALING;

DOCKING PROCEDURES; HOMOLOGY; LIGAND BINDING; PDZ DOMAINS;

PROTEINS;

PDZ PROTEIN; PEPTIDE;

ARTICLE; BINDING SITE; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTAGENESIS; PROTEIN BINDING; PROTEIN DOMAIN; REACTION OPTIMIZATION; VALIDATION PROCESS;

MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 26444604826     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja054195s     Document Type: Article

References (61)

1. Sheng, M.; Sala, C. Annu. Rev. Neurosci. 2001, 24, 1-29.
2. Nourry, C.; Grant, S. G.; Borg, J. P. Sci. STKE 2003, 179, RE7.
3. Hung, A. Y.; Sheng, M. J. Biol. Chem. 2002, 277, 5699-5702.
4. van Ham, M.; Hendriks, W. Mol. Biol. Rep. 2003, 30, 69-82.
5. Beuming, T.; Skrabanek, L.; Niv, M. Y.; Mukherjee, P.; Weinstein, H. Bioinformatics 2005, 21, 827-828.
6. Harris, B. Z.; Millier, B. J.; Lim, W. A. Biochemistry 2001, 40, 5921-5930.
7. Doyle, D. A.; Lee, A.; Lewis, J.; Kim, E.; Sheng, M.; MacKinnon, R. Cell 1996, 85, 1067-1076.
8. Songyang, Z.; Fanning, A. S.; Fu, C.; Xu, J.; Marfatia, S. M.; Chishti, A. H.; Crompton, A.; Chan, A. C.; Anderson, J. M.; Cantley, L. C. Science 1997, 275, 73-77.
9. Bezprozvanny, I.; Maximov, A. FEBS Lett. 2001, 509, 457-462.
10. Chung, H. J.; Xia, J.; Scannevin, R. H.; Zhang, X.; Huganir, R. L. J. Neurosci. 2000, 20, 7258-7267.
11. Parker, L. L.; Backstrom, J. R.; Sanders-Bush, E.; Shieh, B. H. J. Biol. Chem. 2003, 278, 21576-21583.
12. Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. J. Med. Chem. 2004, 47, 558-565.
13. Perola, E.; Walters, W. P.; Charifson, P. S. Proteins 2004, 56, 235-249.
14. Schulz-Gasch, T.; Stahl, M. J. Mol. Model. (Online) 2003, 9, 47-57.
15. Bursulaya, B. D.; Totrov, M.; Abagyan, R.; Brooks, C. L., III. J. Comput. Aided Mol. Des. 2003, 17, 755-763.
16. Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Proteins 2004, 57, 225-242.
17. Totrov, M.; Abagyan, R. Proteins 1997; Suppl 1:215-220.
18. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19, 1639-1662.
19. Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. J. Comput. Aided Mol. Des. 2001, 15, 411-428.
20. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1996, 261, 470-489.
21. Jones, G.; Willen, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J. Mol. Biol. 1997, 267, 727-748.
22. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. J. Med. Chem. 2004, 47, 1739-1749.
23. Jain, A. N. J. Med. Chem. 2003, 46, 499-511.
24. McGann, M. R.; Almond, H. R.; Nicholls, A.; Grant, J. A.; Brown, F. K. Biopolymers 2003, 68, 76-90.
25. Liu, Z.; Dominy, B. N.; Shakhnovich, E. I. J. Am. Chem. Soc. 2004, 126, 8515-8528.
26. Desmet, J.; Wilson, I. A.; Joniau, M.; De Maeyer, M.; Lasters, I. Faseb J. 1997, 11, 164-172.
27. Leach, A. R. J. Mol. Biol. 1994, 235, 345-356.
28. Schaffer, L.; Verkhivker, G. M. Proteins 1998, 33, 295-310.
29. Tong, J. C.; Tan, T. W.; Ranganathan, S. Protein Sci. 2004, 13, 2523-2532.
30. Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. J. Med. Chem. 2004, 47, 45-55.
31. Hillisch, A.; Pineda, L. F.; Hilgenfeld, R. Drug Discov. Today 2004, 9, 659-669.
32. Oshiro, C.; Bradley, E. K.; Eksterowicz, J.; Evensen, E.; Lamb, M. L.; Lanctot, J. K.; Putta, S.; Stanton, R.; Grootenhuis, P. D. J. Med. Chem. 2004, 47, 764-767.
33. Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Proteins 2003, 50, 5-25.
34. McGovern, S. L.; Shoichet, B. K. J. Med. Chem. 2003, 46, 2895-2907.
35. Schafferhans, A.; Klebe, G. J. Mol. Biol. 2001, 307, 407-427.
36. Evers, A.; Gohlke, H.; Klebe, G. J. Mol. Biol. 2003, 334, 327-345.
37. Au, Y.; Atkinson, R. A.; Guerrini, R.; Kelly, G.; Joseph, C.; Martin, S. R.; Muskett, F. W.; Pallavicini, A.; Faulkner, G.; Pastore, A. Structure (Cambridge) 2004, 12, 611-622.
38. Perez, J. L.; Khatri, L.; Chang, C.; Srivastava, S.; Osten, P.; Ziff, E. B. J. Neurosci. 2001, 21, 5417-5428.
39. Zhou, H.; Xu, Y.; Yang, Y.; Huang, A.; Wu, J.; Shi, Y. J. Biol. Chem. 2005, 280, 13841-13847.
40. Brooks, B. R.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
41. Vieth, M.; Hirst, J. D.; Dominy, B. N.; Daigler, H.; Brooks, C. L. J. Comput. Chem. 1998, 19, 1623-1631.
42. Wu, G.; Robertson, D. H.; Brooks, C. L., III; Vieth, M. J. Comput. Chem. 2003, 24, 1549-1562.
43. Wu, G.; Vieth, M. J. Med. Chem. 2004, 47, 3142-3148.
44. Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L., Jr. Protein Sci. 2003, 12, 2001-2014.
45. MacKerell, A. D.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
46. Sadowski, J.; Gasteiger, J.; Klebe, G. J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008.
47. Sali, A.; Potterton, L.; Yuan, F.; van Vlijmen, H.; Karplus, M. Proteins 1995, 23, 318-326.
48. Sanchez, R.; Sali, A. Methods Mol. Biol. 2000, 143, 97-129.
49. Laskowski, R. A., M. M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283-291.
50. Fiser, A.; Sali, A. Bioinformatics 2003, 19, 2500-2501.
51. Karthikeyan, S.; Leung, T.; Birrane, G.; Webster, G.; Ladias, J. A. J. Mol. Biol. 2001, 308, 963-973.
52. Karthikeyan, S.; Leung, T.; Ladias, J. A. J. Biol. Chem. 2002, 277, 18973-18978.
53. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J. Comput. Chem. 2003, 24, 1637-1656.
54. Carlson, H. A. Curr. Opin. Chem. Biol. 2002, 6, 447-452.
55. Mohan, V.; Gibbs, A. C.; Cummings, M. D.; Jaeger, E. P.; DesJarlais, R. L. Curr. Pharm. Des. 2005, 11, 323-333.
56. Madsen, K. L.; Beuming, T.; Niv, M. Y.; Chang, C. W.; Dev, K. K.; Weinstein, H.; Gether, U. J. Biol. Chem. 2005, 280, 20539-20548.
57. Dev, K. K. Nat. Rev. Drug Discov. 2004, 3, 1047-1056.
58. Wojciechowski, M.; Skolnick, J. J. Comput. Chem. 2002, 23, 189-197.
59. Bindewald, E.; Skolnick, J. J. Comput. Chem. 2005, 26, 374-383.
60. Vakser, I. A. Biopolymers 1996, 39, 455-464.
61. Kay, B. K.; Kehoe, J. W. Chem. Biol. 2004, 11, 423-425.