Cooperative motions of protein and hydration water molecules: Molecular dynamics study of scytalone dehydratase

Journal of the American Chemical Society

Volumn 126, Issue 40, 2004, Pages 13132-13139

  Okimoto, Noriaki ^a   Nakamura, Takashi ^b   Suenaga, Atsushi ^c   Futatsugi, Noriyuki ^c   Hirano, Yoshinori ^a   Yamaguchi, Isamu ^b   Ebisuzaki, Toshikazu ^a  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b Elements Chemistry Laboratory   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; HYDRATION; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE;

COOPERATIVE MOTIONS; LIGAND-BINDING POCKETS;

ENZYMES;

HYDROLYASE; MELANIN; PROTEIN; SCYTALONE DEHYDRATASE; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STRUCTURE; FUNGUS; HYDRATION; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOTION; PRINCIPAL COMPONENT ANALYSIS; RICE BLAST; SOLVATION; X RAY CRYSTALLOGRAPHY;

EID: 5644282595     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja048053u     Document Type: Article

References (35)

1. Dill, K. A. Biochemistry 1990, 29, 7133-7155.
2. Ferrand, M.; Dianoux, A. J.; Petry, W.; Zaccai, G. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9668-9672.
3. Gerstein, M.; Chothia, C. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10167-10172.
4. Hayward, S.; Kitao, A.; Hirata, F.; Go, N. J. Mol. Biol. 1993, 234, 1207-1217.
5. Higo, J.; Sasai, M.; Shirai, H.; Nakamura, H.; Kugimiya, T. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5961-5964.
6. Kitao, A.; Hirata, F.; Go, N. J. Phys. Chem. 1993, 97, 10223-10230.
7. Okimoto, N.; Tsukui, T.; Kitayama, K.; Hata, M.; Hoshino, T.; Tsuda, M. J. Am. Chem. Soc. 2000, 122, 5613-5622.
8. Nakasako, M.; Fujisawa, T.; Adachi, S.; Kudo, T.; Higuchi, S. Biochemistry 2001, 40, 3069-3079.
9. Chen, J. M.; Xu, S. L.; Wawrzak, Z.; Basarab, G. S.; Jordan, D. B. Biochemistry 1998, 37, 17735-17744.
10. Basarab, G. S.; Steffens, J. J.; Wawrzak, Z.; Schwartz, R. S.; Lundqvist, T.; Jordan, D. B. Biochemistry 1999, 38, 6012-6024.
11. Motoyama, T.; Imanishi, K.; Yamaguchi, I. Biosci. Biotechnol. Biochem. 1998, 62, 564-566.
12. Lundqvist, T.; Rice, J.; Hodge, C. N.; Basarab, G. S.; Pierce, J.; Lindqvist, Y. Structure 1994, 2, 937-944.
13. Nakasako, M.; Motoyama, T.; Kurahashi, Y.; Yamaguchi, I. Biochemistry 1998, 37, 9931-9939.
14. Wawrzak, Z.; Sandalova, T.; Steffens, J. J.; Basarab, G. S.; Lundqvist, T.; Lindqvist, Y.; Jordan, D. B. Proteins 1999, 35, 425-439.
15. Motoyama, T.; Nakasako, M.; Yamaguchi, I. Acta Crystallogr., Sect. D Biol. Crystallogr. 2002, 58, 148-150.
16. Kollman, P. A.; Dixon, R.; Cornell, W.; Fox, T.; Chipot, C.; Pohorille, A. In Computer Simulation of Biomolecular System; Wilkinson, A., Weiner, P., Van Gunsteren, W., Eds.; Elsevier: The Netherlands, 1997; pp 83-96.
17. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Mont-gomery, J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millan, J. M.; Daniel, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morlkuma, K.; Malick, D. K.; Robuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Oritiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M.; Peng, C. Y.; Nanayakkara, A.; Gonzakez, C.; Challacombe, M.; Gill, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian98, Revision A.lx; Gaussian, Inc.: Pittsburgh, PA, 2001.
18. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J. Phys. Chem. 1993, 7(40), 10269-10280.
19. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. J. Chem. Phys. 1983, 79, 926-935.
20. Narumi, T.; Susukita, R.; Ebisuzaki, T.; McNiven, G.; Elmegreen, B. Mol. Simul. 1999, 21, 401-415.
21. Susukita, R.; Ebisuzaki, T.; Elmegreen, B. G.; Furasawa, H.; Kalo, K.; Kawai, A.; Kobayashi, Y.; Koishi, T.; McNiven, G. D.; Narumi, T.; Yasuoka, K. Comput. Phys. Comm. 2003, 155, 115-131.
22. Fujii, Y.; Okimoto, N.; Hata, M.; Narumi, T.; Yasuoka, K.; Susukita, R.; Suenaga, A.; Futatsugi, N.; Koishi, T.; Furusawa, H.; Kawai, A.; Ebisuzaki, T.; Neya, S.; Hoshino, T. J. Phys. Chem. B 2003, 107, 10274-10283.
23. Okimoto, N.; Yamanaka, K.; Suenaga, A.; Hirano, Y.; Futatsugi, N.; Narumi, T.; Yasuoka, K.; Susukita, R.; Koishi, T.; Furasawa, H.; Kawai, A.; Hata, M.; Hoshino, T.; Ebisuzaki, T. Chem-Bio. Informatisc. J. 2003, 3, 1-11.
24. Suenaga, A.; Hatakeyama, M.; Ichikawa, M.; Yu, X.; Futatsugi, N.; Narumi, T.; Fukui, K.; Terada, T.; Taiji, M.; Shirouzu M.; Yokoyama, S.; Konagaya, A. Biochemistry 2003, 42, 5195-5200.
25. Suenaga, A.; Kiyatkin, A. B.; Hatakeyama, M.; Futatsugi, N.; Okimoto, N.; Hirano, Y.; Narumi, T.; Kawai, A.; Susukita, R.; Koishi, T.; Furasawa, H.; Yasuoka, K.; Takada, N.; Ohno, Y.; Taiji, M.; Ebisuzaki, T.; Hoek, J. B.; Konagaya, A.; Kholodenko, B. N. J. Biol. Chem. 2004, 279, 4657-4662.
26. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 6; University of California, San Francisco: San Francisco, CA, 1999.
27. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
28. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
29. Kitao, A.; Hirata, F.; Go, N. Chem. Phys. 1991, 158, 447-472.
30. Kitao, A.; Go, N. Curr. Opin. Struct. Biol. 1999, 9, 164-169.
31. Sanner, M. F.; Olson, A. J.; Spehner, J. C. Biopolymers 1996, 38, 305-320.
32. Rocchia, W.; Alexov E.; Honig, B. J. Phys. Chem. B 2001, 105, 6507-6514.
33. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. J. Comput. Chem. 2002, 23, 128-137.
34. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
35. Liou, H. L.; Storch, J. Biochemistry 2001, 40, 6475-6485.