Brownian dynamics simulation of protein-protein diffusional encounter

Methods: A Companion to Methods in Enzymology

Volumn 14, Issue 3, 1998, Pages 329-341

  Gabdoulline, Razif R ^a   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME INHIBITOR; MUTANT PROTEIN; PROTEIN; RIBONUCLEASE;

ARTICLE; DIFFUSION; ELECTRICITY; ENZYME INHIBITOR INTERACTION; IONIC STRENGTH; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

EID: 0031714012     PISSN: 10462023     EISSN: None     Source Type: Journal    
DOI: 10.1006/meth.1998.0588     Document Type: Article

References (55)

1. Calef, D. F., and Deutch, M. (1983) Annu. Rev. Phys. Chem. 34, 493-524.
2. Berg, O. G., and vonHippel, P. H. (1985) Annu. Rev. Biophys. Biophys. Chem. 14, 131-160.
3. DeLisi, C. (1980) Q. Rev. Biophys. 13, 201-230.
4. Szabo, A., Stolz, L., and Granzow, R. (1995) Curr. Opin. Struct. Biol. 5, 699-705.
5. Malmqvist, M. (1993) Curr. Opin. Immunol. 5, 282-286.
6. Stone, S. R., Dennis, S., and Hofsteenge, J. (1986) Biochemistry 28, 6857-6863.
7. Schreiber, G., and Fersht, A. R. (1996) Nature Struct. Biol. 3, 427-431.
8. Gosting, L. J. (1956) Adv. Protein Chem. 11, 429-554.
9. Johnstone, R. W., Andrew, S. M., Hogarth, M. P., Pietersz, G. A., and McKenzie, I. F. C. (1990) Mol. Immunol. 27, 327-333.
10. Ito, W., Yasui, H., and Kurosawa, Y. (1995) J. Mol. Biol. 248, 729-732.
11. Madura, J. D., Briggs, J. M., Wade, R. C., Davis, M. E., Luty, B. A., Ilin, A., Antosiewicz, J., Gilson, M. K., Bagheri, B., Scott, L. R., and McCammon, J. A. (1995) Comp. Phys. Commun. 91, 57-95.
12. Wade, R. C. (1996) Biochem. Soc. Trans. 24, 254-259.
13. Getzoff, E. D., Cabelli, D. E., Fisher, C. L., Parge, H. E., Viezzoli, M. S., Banci, L., and Hallewell, R. A. (1992) Nature 358, 347-351.
14. Northrup, S. H., and Erickson, H. P. (1992) Proc. Natl. Acad. Sci. USA 89, 3338-3342.
15. Einstein, A. (1905) Ann. Phys. (Leipzig) 17, 549.
16. Smoluchowski, M. V. (1906) Ann. Phys. (Leipzig) 21, 756.
17. Madura, J. D., Briggs, J. M., Wade, R. C., and Gabdoulline, R. R. (1997) Encyclopedia of Computational Chemistry, in press.
18. Ermak, D. L., and McCammon, J. A. (1978) J. Chem. Phys. 69, 1352-1360.
19. Smoluchowski, M. V. (1917) Z. Phys. Chem. 92, 129-168.
20. Northrup, S. H., Allison, S. A., and McCammon, J. A. (1984) J. Chem. Phys. 80, 1517-1524.
21. Huber, G. A., and Kim, S. (1996) Biophys. J. 70, 97-110.
22. Zhou, H.-X. (1990) J. Phys. Chem. 94, 8794-8800.
23. Luty, B. A., McCammon, J. A., and Zhou, H.-X. (1992) J. Chem. Phys. 97, 5682-5686.
24. Zhou, H.-X. (1993) Biophys. J. 64, 111-1726.
25. Luty, B. A., Wade, R. C., Madura, J. D., Davis, M. E., Briggs, J. M., and McCammon, J. A. (1993) J. Phys. Chem. 97, 233-237.
26. Northrup, S. H., Reynolds, J. C. L., Miller, C. M., Forrest, K. J., and Boles, J. O. (1986) J. Am. Chem. Soc. 108, 8162-8170.
27. Davis, M. E., and McCammon, J. A. (1989) J. Comp. Chem. 10, 386-391.
28. Gabdoulline, R. R., and Wade, R. C. (1996) J. Phys. Chem. 100, 3868-3878.
29. DelaTorre, J. G., and Bloomfield, V. A. (1981) Q. Rev. Biophys. 14, 81-139.
30. Antosiewicz, J., Gilson, M. K., Lee, I. H., and McCammon, J. A. (1995) Biophys. J. 68, 62-68.
31. Wolynes, P. G., and Deutch, J. M. (1976) J. Chem. Phys. 65, 450-454.
32. Friedman, H. L. (1966) J. Phys. Chem. 70, 3931-3933.
33. Allison, S. A., Srinivasan, N., McCammon, J. A., and Nortrup, S. H. (1984) J. Phys. Chem. 88, 6152-6157.
34. Deutch, J. L., and Felderhof, B. U. (1973) J. Chem. Phys. 59, 1669-1671.
35. Brune, D., and Kim, S. (1994) Proc. Natl. Acad. USA 91, 2930-2934.
36. Gabdoulline, R. R., and Wade, R. C. (1997) Biophys. J. 72, 1917-1929.
37. Wade, R. C., Davis, M. E., Luty, B. A., Madura, J. D., and McCammon, J. A. (1993) Biophys. J. 64, 9-15.
38. Demchuk, E., and Wade, R. C. (1996) J. Phys. Chem. 100, 17373-17387.
39. Hooft, R. W., Sander, C., and Vriend, G. (1996) Proteins 26, 363-376.
40. Jorgensen, W., and Tirado-Rives, J. (1988) J. Am. Chem. Soc. 110, 1657-1666.
41. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) J. Comp. Chem. 4, 187-217.
42. Sharp, K. A., and Honig, B. (1990) Annu. Rev. Biophys. Chem. 19, 301-332.
43. Northrup, S. H., Boles, J. O., and Reynolds, J. C. L. (1987) J. Phys. Chem. 91, 5991-5998.
44. Northrup, S. H., Boles, J. O., and Reynolds, J. C. L. (1988) Science 241, 67-70.
45. Northrup, S. H., Thomasson, K. A., Miller, C. M., Barker, P. D., Eltis, L. D., Guillemette, J. G., Inglis, S. C., and Mauk, A. G. (1993) Biochemistry 32, 6613-6623.
46. Antosiewicz, J., and Porschke, D. (1989) J. Phys. Chem. 93, 5301.
47. Brune, D., and Kim, S. (1993) Proc. Natl. Acad. Sci. USA 90, 3835-3839.
48. Antosiewicz, J., Briggs, J. M., and McCammon, J. A. (1996) Eur. Biophys. J. 24, 137-141.
49. Zhou, H.-X. (1996) J. Chem. Phys. 105, 7235-7237.
50. Pelletier, H., and Kraut, J. (1992) Science 258, 1748-1755.
51. Kozack, R. E., and Subramaniam, S. (1993) Protein Sci. 2, 915-926.
52. Kozack, R. E., d'Mello, M. J., and Subramaniam, S. (1995) Biophys. J. 68, 807-814.
53. Nambi, P., Wierzbicki, A., and Allison, S. A. (1991) J. Phys. Chem. 95, 9595-9600.
54. Sommer, J., Jonah, C., Fukuda, R., and Bersohn, R. (1982) J. Mol. Biol. 159, 721.
55. Zhou, H.-X., Briggs, J. M., and McCammon, J. A. (1996) J. Am. Chem. Soc. 118, 13069-13070.