Implementation of π-π interactions in molecular dynamics simulation

Journal of Computational Chemistry

Volumn 28, Issue 6, 2007, Pages 1091-1099

  Yuki, Hitomi ^a   Tanaka, Yoshikazu ^a   Hata, Masayuki ^a   Ishikawa, Hidenori ^a   Neya, Saburo ^a   Hoshino, Tyuji ^a,b  

^a CHIBA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

interaction; Drugbinding conformation; Molecular dynamics simulation; Morse type potential function; Protein structure

Indexed keywords

Π-Π INTERACTION; DRUGBINDING CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MORSE TYPE POTENTIAL FUNCTION; PROTEIN STRUCTURE;

BIOMOLECULES; COMPUTER SIMULATION; DATA REDUCTION; FUNCTION EVALUATION; GEOMETRY; PROTEIN FOLDING;

MOLECULAR DYNAMICS;

CARBAMAZEPINE; CYP3A4 PROTEIN, HUMAN; CYTOCHROME P450; PEPTIDE; TRP CAGE PEPTIDE; TRP-CAGE PEPTIDE; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MOTIF; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; CARBAMAZEPINE; COMPUTER SIMULATION; CYTOCHROME P-450 ENZYME SYSTEM; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 33947720252     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20557     Document Type: Article

References (31)

1. Hunter, C. A. J Mol Biol 1993, 230, 1025.
2. Samanta, U.; Pal, D.; Chakrabarti, P. Proteins 2000, 38, 288.
3. Evans, D. A.; Chapman, K. T.; Hung, K. T.; Kawaguchi, A. T. Angew Chem Int Ed Engl 1987, 26, 1184.
4. Burley, S. K.; Petsko, G. A. Science 1985, 229, 23.
5. Mitchell, J. B.; Nandi, C. L.; McDonald, I. K.; Thrnton, J. M. J Mol Biol 1994, 239, 315.
6. Kashima, A.; Inoue, Y.; Sugio, S.; Maeda, I.; Nose, T.; Shimohigashi, Y. Eur J Biochem 1998, 255, 12.
7. Kryger, G.; Silman, I.; Sussman, J. L. Struct Fold Des 1999, 7, 297.
8. Williams, P. A.; Cosme, J.; Vinkovic, D. M.; Ward, A.; Angove, H. C.; Day, P. J.; Vonrhein, C.; Tickle, I. J.; Jhoti, H. Science 2004, 305, 683.
9. Williams, P. A.; Cosme, J.; Ward, A.; Angove, H. C.; Vinkovic, D. M.; Jhoti, H. Nature 2003, 424, 464.
10. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J Am Chem Soc 2002, 124, 104.
11. Macias, A. T.; Mackerell, A. D., Jr. J Comput Chem 2005, 26, 1452.
12. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J Am Chem Soc 2000, 122, 11450.
13. Sinnokrot, M. O.; Sherrill, C. D. J Am Chem Soc 2004, 126, 7690.
14. Sinnokrot, M. O.; Sherrill, C. D. J Phys Chem A 2004, 108, 10200.
15. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Carnmi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, 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. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A.11; Gaussian: Pittsburgh, PA, 1998.
16. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. H.; Weiner, P.; Kollman, P. A. AMBER 7.0; University of California: San Francisco, 2002.
17. Cochran, A. G.; Skelton, N. J.; Starovasnik, M. A. Proc Natl Acad Sci USA 2001, 98, 5578.
18. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Nat Struct Biol 2002, 9, 425.
19. McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nat Struct Biol 1997, 4, 180.
20. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
21. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
22. Wang, J.; Cieplak, P.; Kollman, P. A. J Comput Chem 2000, 21, 1049.
23. Ode, H.; Ota, M.; Neya, S.; Hata, M.; Sugiura, W.; Hoshino, T. J Phys Chem B 2005, 109, 564.
24. Sato, Y.; Hata, M.; Neya, S.; Hoshino, T. Protein Sci 2005, 14, 183.
25. Mori, K.; Hata, M.; Neya, S.; Hoshino, T. Chem Bio Inform J 2004, 4, 15.
26. Okimoto, N.; Yamanaka, K.; Suenaga, A.; Hata, M.; Hoshino, T. Biophys J 2002, 82, 2746.
27. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
28. Vermeulen, W.; Vanhaesebrouck, P.; Van Troys, M.; Verschueren, M.; Fant, F.; Goethals, M.; Ampe, C.; Martins, J. C.; Borremans, F. A. M. Protein Sci 2004, 13, 1276.
29. Torimoto, N.; Ishii, I.; Hata, M.; Nakamura, H.; Imada, H.; Ariyoshi, N.; Ohmori, S.; Igarashi, T.; Kitada, M. Biochemistry 2003, 42, 15068.
30. Yano, J. K.; Wester, M. R.; Schoch, G. A.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. J Biol Chem 2004, 279, 38091.
31. Haines, D. C.; Tomchick, D. R.; Machius, M.; Peterson, J. A. Biochemistry 2001, 40, 13456.