Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies

Journal of the American Chemical Society

Volumn 121, Issue 36, 1999, Pages 8133-8143

  Massova, Irina ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ORGANIC COMPOUND; PROTEIN P53;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; MATHEMATICAL ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; SIMULATION;

EID: 0033568644     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja990935j     Document Type: Article

References (33)

1. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401-9409.
2. The program will be distributed with the AMBER6 release.
3. Cieplak, P.; Kollman, P. A. DNA-Ligand interactions; work in progress; and Chong, L. T. et al., Amibody-Ligand Interactions. Submitted for publication.
4. Cieplak, P.; Kollman, P. A. DNA-Ligand interactions; work in progress; and Chong, L. T. et al., Amibody-Ligand Interactions. Submitted for publication.
5. Abbreviations: hMdm2, human Mdm2; xMdm2, Xenopus laevis Mdm2.
6. Kastan, M. B.; Onyekwere, O.; Sidransky, D.; Vogelstein, B.; Craig, R. W. Cancer Res. 1991, 51, 6304-6311.
7. Lane, D. P. Nature 1992, 358, 15-16.
8. Kuerbitz, S. J.; Plunkett, B. S.; Walsh, W. V.; Kastan, M. B. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 7491-7495.
9. Graeber, T. G.; Peterson, J. F.; Tsai, M.; Monica, K.; Fornace, A. J., Jr.; Giaccia, A. J. Mol. Cell Biol. 1994, 14, 6264-6277.
10. Linke, S. P.; Clarkin, K. C.; Di Leonardo, A.; Tsou, A.; Wahl, G. M. Genes Dev. 1996, 10, 934-947.
11. Schwartz, J. L.; Antoniades, D. Z.; Zhao, S. Ann. N.Y. Acad. Sci. 1993, 686, 262-278.
12. Debbas, M.; White, E. Genes Dev. 1993, 7, 546-554.
13. Sinkovics, J. G. Acta Microbiol. Hung. 1991, 38, 321-334.
14. Giaccia, A. J.; Kastan, M. B. Genes Dev. 1998, 12, 2973-2983.
15. Bennett, M.; Macdonald, K.; Chan, S. W.; Luzio, J. P.; Simari, R.; Weissberg, P. Science 1998, 282, 290-293.
16. Symonds, H.; Krall, L.; Remington, L.; Saenz-Robles, M.; Lowe, S.; Jacks, T.; Van Dyke, T. Cell 1994, 78, 703-711.
17. Kaelin, W. G. Science 1998, 281, 57-58.
18. Oliner, J. D.; Kinzler, K. W.; Meltzer, P. S.; George, D. L.; Vogelstein, B. Nature 1992, 358, 80-83.
19. Sun, P.; Dong, P.; Dai, K.; Hannon, G. J.; Beach, D. Science 1998, 282, 2270-2272.
20. Kussie, P. H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.; Levine, A. J.; Pavletich, N. P. Science 1996, 274, 948-953.
21. Böttger, A.; Böttger, V.; Garcia-Echeverria, C.; Chène, P.; Hochkeppel, H. K.; Sampson, W.; Ang, K.; Howard, S. F.; Picksley, S. M.; Lane, D. P. J. Mol. Biol. 1997, 269, 744-756.
22. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
23. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
24. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
25. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
26. Sanner, M. F.; Olson, A. J.; Spehner, J. C. Biopolymers 1996, 38, 305-320.
27. Clackson, T.; Ultsch, M. H.; Wells, J. A.; de Vos, A. M. J. Mol. Biol. 1998, 277, 1111-1128.
28. Cunningham, B. C.; Wells, J. A. Science 1989, 244, 1081-1085.
29. Jones, S.; Thornton, J. M. J. Mol. Biol. 1997, 272, 121-132.
30. Lin, J.; Chen, J.; Elenbaas, B.; Levine, A. J. Genes Dev. 1994, 8, 1235-1246.
31. Radmer, R. J.; Kollman, P. A. J. Comput.-Aided Mol. Des. 1998, 12, 215-227.
32. Reyes, C. M.; Kollman, P. A. J. Mol. Biol. Submitted for publication.
33. Huo, S.; Massova, I.; Kollman, P. A. Studies in progress.