Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design

Current Topics in Medicinal Chemistry

Volumn 7, Issue 10, 2007, Pages 999-1005

  Ma, Buyong ^a   Nussinov, Ruth ^a,b  

^a SAIC FREDERICK INC   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Amyloid; Drug design; Hot spot; Protein binding site; Protein protein interactions

Indexed keywords

AMYLOID PROTEIN; CD4 ANTIGEN; DRUG; GLYCOPROTEIN GP 120; GLYCOPROTEIN GP 41; ISOLEUCINE; LYSINE; METHIONINE; PHENYLALANINE; PROTEIN MDM2; PROTEIN P53; PROTEIN P66; TRANSCRIPTASE; TRANSCRIPTION FACTOR; TRYPTOPHAN; VIRUS PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; BINDING AFFINITY; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; DIMERIZATION; DRUG DESIGN; DRUG RESEARCH; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; PROTEIN TARGETING; REVIEW; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; VIRUS STRAIN;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMYLOID; ANIMALS; BINDING SITES; DRUG DESIGN; GENE PRODUCTS, ENV; HUMANS; METHIONINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHENYLALANINE; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SEQUENCE ALIGNMENT; TRYPTOPHAN; TUMOR SUPPRESSOR PROTEIN P53;

EID: 34447286664     PISSN: 15680266     EISSN: None     Source Type: Journal    
DOI: 10.2174/156802607780906717     Document Type: Review

References (44)

1. Ryan, D. P.; Matthews, J. M. Curr. Opin. Struct. Biol., 2005, 15, 441-6.
2. Sillerud, L. O.; Larson, R. S. Curr. Protein Pept. Sci., 2005, 6, 151-69.
3. Pommier, Y.; Cherfils, J. Trends Pharmacol. Sci., 2005, 26, 138-45.
4. Zhao, L.; Chmielewski, J. Curr. Opin. Struct. Biol., 2005, 15, 31-4.
5. Loregian, A.; Palu, G. J. Cell Physiol., 2005, 204, 750-62.
6. Arkin, M. R.; Wells, J. A. Nat. Rev. Drug Discov., 2004, 3, 301-17.
7. Fry, D. C.; Vassilev, L. T. J. Mol. Med., 2005, 83, 955-63.
8. Yin, H.; Hamilton, A. D. Angew. Chem. Int. Ed. Engl., 2005, 44, 4130-63.
9. Kennedy, D.; Norman, C. Science, 2005, 309, 75.
10. Nooren, I. M.; Thornton, J. M. J. Mol. Biol., 2003, 325, 991-1018.
11. Jones, S.; Thornton, J. M. J. Mol. Biol., 1997, 272, 133-43.
12. Janin, J.; Wodak, S. J. Adv. Protein Chem., 2002, 61, 1-8.
13. Ma, B.; Pan, Y.; Gunasekaran, K.; Keskin, O.; Venkatara-ghavan, R. B.; Levine, A. J.; Nussinov, R. Phys. Biol., 2005, 2, S56-66.
14. Bogan, A. A.; Thorn, K. S. J. Mol. Biol., 1998, 280, 1-9.
15. Ma, B.; Elkayam, T.; Wolfson, H.; Nussinov, R. Proc. Natl. Acad. Sci. USA, 2003, 100, 5772-7.
16. Ma, B.; Wolfson, H. J.; Nussinov, R. Curr Opin Struct Biol, 2001, 11, 364-9.
17. DeLano, W. L. Curr. Opin. Struct. Biol., 2002, 12, 14-20.
18. Res, I.; Lichtarge, O. Phys. Biol., 2005, 2, S36-43.
19. Magliery, T. J.; Regan, L. BMC Bioinformatics, 2005, 6, 240.
20. del Sol, A.; O'Meara, P. Proteins, 2005, 58, 672-82.
21. Mansfield, K. L.; Johnson, N.; Fooks, A. R. J. Gen. Virol., 2004, 85, 3279-83.
22. Zhang, Z.; Palzkill, T. J. Biol. Chem., 2003, 278, 45706-12.
23. Schultz, A.; Ling, M.; Larsson, C. J. Biol. Chem., 2004, 279, 31750-60.
24. Vassilev, L. T.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C.; Fotouhi, N.; Liu, E. A. Science, 2004, 303, 844-8.
25. Cho, Y.; Gorina, S.; Jeffrey, P. D.; Pavletich, N. P. Science, 1994, 265, 346-55.
26. Derbyshire, D. J.; Basu, B. P.; Serpell, L. C.; Joo, W. S.; Date, T.; Iwabuchi, K.; Doherty, A. J. EMBO J., 2002, 21, 3863-72.
27. Gorina, S.; Pavletich, N. P. Science, 1996, 274, 1001-5.
28. Kwong, P. D.; Wyatt, R.; Robinson, J.; Sweet, R. W.; Sodroski, J.; Hendrickson, W. A. Nature, 1998, 393, 648-59.
29. Pan, Y.; Ma, B.; Keskin, O.; Nussinov, R. J. Biol. Chem., 2004, 279, 30523-30.
30. Xiang, S. H.; Kwong, P. D.; Gupta, R.; Rizzuto, C. D.; Casper, D. J.; Wyatt, R.; Wang, L.; Hendrickson, W. A.; Doyle, M. L.; Sodroski, J. J. Virol., 2002, 76, 9888-99.
31. Root, M. J.; Kay, M. S.; Kim, P. S. Science, 2001, 291, 884-8.
32. Clore, G. M.; Ernst, J.; Clubb, R.; Omichinski, J. G.; Kennedy, W. M.; Sakaguchi, K.; Appella, E.; Gronenborn, A. M. Nat. Struct. Biol., 1995, 2, 321-33.
33. Mulky, A.; Sarafianos, S. G.; Jia, Y.; Arnold, E.; Kappes, J. C. J. Mol. Biol., 2005, 349, 673-84.
34. Soldi, G.; Bemporad, F.; Torrassa, S.; Relini, A.; Ramazzotti, M.; Taddei, N.; Chiti, F. Biophys. J., 2005, 89, 4234-44.
35. Pawar, A. P.; Dubay, K. F.; Zurdo, J.; Chiti, F.; Vendruscolo, M.; Dobson, C. M. J. Mol. Biol., 2005, 350, 379-92.
36. Sanchez de Groot, N.; Pallares, I.; Aviles, F. X.; Vendrell, J.; Ventura, S. BMC Struct. Biol., 2005, 5, 18.
37. Quijano, F. A. R.; Morrow, D.; Wise, B. M.; Brancia, F. L.; Goux, W. J. Biochemistry, 2006, 45, 4638-4652.
38. Gazit, E. FASEB J., 2002, 16, 77-83.
39. Bemporad, F.; Taddei, N.; Stefani, M.; Chiti, F. Protein Sci., 2006, 15, 862-70.
40. Reches, M.; Gazit, E. Science, 2003, 300, 625-7.
41. Sato, T.; Kienlen-Campard, P.; Ahmed, M.; Liu, W.; Li, H.; Elliott, J. I.; Aimoto, S.; Constantinescu, S. N.; Octave, J. N.; Smith, S. O. Biochemistry, 2006, 45, 5503-5516.
42. Lopez de la Paz, M.; Serrano, L. Proc. Natl. Acad. Sci. USA, 2004, 101, 87-92.
43. Ma, B.; Nussinov, R. Biophys. J., 2006, 90, 3365-74.
44. de Groot, N. S.; Aviles, F. X.; Vendrell, J.; Ventura, S. FEBS J., 2006, 273, 658-68.