Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-Cope rearrangement

Journal of the American Chemical Society

Volumn 124, Issue 42, 2002, Pages 12535-12542

  Asada, Toshio ^a   Gouda, Hiroaki ^a   Kollman, Peter A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Osaka Prefecture University   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITY;

ANTIBODIES; CATALYSIS; COMPUTER SIMULATION; ELECTROSTATICS; MUTAGENESIS;

MOLECULAR DYNAMICS;

ALANINE; ANTIBODY; ARGININE; ASPARAGINE; ASPARTIC ACID; AZ28 ANTIBODY; CATALYTIC ANTIBODY; GLUTAMINE; GLYCINE; HAPTEN; HISTIDINE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARTICLE; CATALYSIS; CORRELATION ANALYSIS; GERM LINE; MODEL; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; REACTION ANALYSIS;

ALANINE; ANTIBODIES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; GLYCINE; HAPTENS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 0037164076     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja020774a     Document Type: Article

References (34)

1. Yang, P. L.; Schultz, P. G. J. Mol. Biol. 1999, 294, 1191-1201.
2. Fox, T.; Scanlan, T. S.; Kollman, P. A. J. Am. Chem. Soc. 1997, 119, 11571-11577.
3. Allen, D.; Cumano, A.; Simon, T.; Sablitzky, F.; Rajewsky, K. Int. J. Cancer Suppl. 1988, 3, 1-8.
4. Ulrich, H. D.; Mundorff, E.; Santarsiero, B. D.; Driggers, E. M.; Stevens, R. C.; Schultz, P. G. Nature 1997, 389, 271-275.
5. Mundorff, E. C.; Hanson, M. A.; Varvak, A.; Ulrich, H.; Schultz, P. G.; Stevens, R. C. Biochemistry 2000, 39, 627-632.
6. Dewar, M. J. S.; Wade, L. E. J. J. Am. Chem. Soc. 1975, 99, 4417-4424.
7. Baumann, H.; Chen, P. Helv. Chim. Acta 2001, 84, 124-140.
8. Hrovat, D. A.; Beno, B. R.; Lange, H.; Yoo, H.-Y.; Houk, K. N.; Borden, W. T. J. Am. Chem. Soc. 1999, 121, 10529-10537.
9. Haeffner, F.; Houk, K. N.; Reddy, Y. R.; Paquette, L. A. J. Am. Chem. Soc. 1999, 121, 11880-11884.
10. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. Amber 6, 6th Ed.; University of California at San Francisco: San Francisco, 1999.
11. Srinivasan, J.; Miller, J.; Kollman, P. A.; Case, D. A. J. Biomol. Struct. Dyn. 1998, 16, 671-682.
12. Massova, I.; Kollman, P. A. Perspect. Drug Discovery Des. 2000, 18, 113-135.
13. Chong, L. T.; Duan, Y.; Wang, L.; Massova, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14330-14335.
14. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Acc. Chem. Res. 2000, 33, 889-897.
15. Lee, M. R.; Duan, Y.; Kollman, P. A. Proteins: Struct., Funct., Genet. 2000, 39, 309-316.
16. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568.
17. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
18. Massova, I.; Kollman, P. A. J. Am. Chem. Soc. 1999, 121, 8133-8143.
19. Dixon, R. W.; Kollman, P. Proteins: Struct., Funct., Genet. 1999, 36, 471-473.
20. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 3909-3916.
21. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
22. Stanton, R. V.; Perakyla, M.; Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 3448-3457.
23. Frish, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Strain, M. C.; Burant, J. C.; Stratmann, R. E.; Dapprich, S.; Kudin, K. N.; Millan, J. M.; Daniel, A. D.; Petersson, G. A.; Montgomery, J. A.; Zakrzewski, V. G.; Raghavachari, K.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Barone, V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Stewart, J. P.; Gonzales, C.; Head-Gordon, M.; Gill, P. M. W.; Johnson, B. G.; Pople, J. A. Gaussian 98; Gaussian: Pittsburgh, PA, 1998.
24. Matsubara, T.; Maseras, F.; Koga, N.; Morokuma, K. J. Phys. Chem. 1996, 100, 2573-2580.
25. Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. J. Mol. Struct. (THEOCHEM) 1999, 461-462, 1-21.
26. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
27. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J. Am. Chem. Soc. 1993, 115, 9620-9631.
28. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
29. Guenot, J.; Kollman, P. A. J. Comput. Chem. 1993, 14, 295-311.
30. Nicholls, A.; Honig, B. J. Comput. Chem. 1991, 12, 435-445.
31. Sitkoff, D.; Sharpe, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
32. Sanner, M. F.; Olson, A. J.; Spehner, J.-C. Biopolymers 1996, 38, 305-320.
33. Doering, W. v. E.; Toscano, V. G.; Beasley, G. H. Tetrahedron 1971, 27, 5299.
34. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 2589-2596.