The use of time-averaged 3JHH Restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: Methodology and applications

Journal of Computational Chemistry

Volumn 31, Issue 3, 2010, Pages 561-572

  Hendrickx, Pieter M S ^a   Corzana, Francisco ^b   Depraetere, Stefaan ^c   Tourwe, Dirk A ^d   Augustyns, Koen ^c   Martins, José C ^a  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF LA RIOJA   (Spain)

^c UNIVERSITY OF ANTWERP   (Belgium)

^d VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

Conformational analysis; Molecular modeling; NMR; Nucleosides; Pseudorotation; Ribose; Time averaged restraints

Indexed keywords

ANALYSIS APPROACH; COMPUTATIONAL BURDEN; CONFORMATIONAL ANALYSIS; CONFORMATIONAL BEHAVIOR; EXPERIMENTAL DATA; FITTING ERROR; FITTING PROCEDURE; FIVE-MEMBERED RINGS; FORCE FIELDS; MATHEMATICAL PROCEDURES; MD SIMULATION; MODEL COMPOUND; MODELING PARAMETERS; MOLECULAR DYNAMICS SIMULATIONS; PSEUDOROTATION; SCALAR COUPLING; SOLUTION SPACE; TIME-AVERAGED;

BIOMOLECULES; ERROR ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOLECULES; NUCLEAR MAGNETIC RESONANCE; TAR;

CONFORMATIONS;

DRUG DERIVATIVE; NUCLEOSIDE; RIBOSE;

ARTICLE; CHEMISTRY; CONFORMATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; QUANTUM THEORY; SOLUTION AND SOLUBILITY; THERMODYNAMICS; TIME;

MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; NUCLEOSIDES; QUANTUM THEORY; RIBOSE; SOLUTIONS; THERMODYNAMICS; TIME FACTORS;

EID: 75649102865     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21345     Document Type: Article

References (36)

1. Altona, C.; Sundaralingam, M. J Am Chem Soc 1972, 94, 8205.
2. van Wijk, J.; Haasnoot, C. A. G.; de Leeuw, F. A. A. M.; Huckriede, B. D.; Westra Hoekzema, A.; Altona, C. PSEUROT 6.2; Leiden Institute of Chemistry: Leiden University, 1993.
3. de Leeuw, F. A. A. M.; Altona, C. J Comput Chem 1983, 4, 428.
4. Houseknecht, J. B.; Altona, C.; Hadad, C. M.; Lowary, T. L. J Org Chem 2002, 67, 4647.
5. Church, T.; Carmichael, I.; Serianni, S. J Am Chem Soc 1997, 119, 8946.
6. Freier, S.; Altmann, K.-H. Nucleic Acids Res 1997, 25, 4429.
7. Eldrup, A. B.; Allerson, C. R.; Bennett, C. F.; Bera, S.; Bhat, B.; Bhat, N.; Bosserman, M. R.; Brooks, J.; Burlein, C.; Carroll, S. S.; Cook, P. D.; Getty, K. L.; MacCoss, M.; McMasters, D. R.; Olsen, D. B.; Prakash, T. P.; Prhavc, M.; Song, Q.; Tomassini, J. E.; Xia J. J Med Chem 2004, 47, 2283.
8. Cappellacci, L.; Barboni, G.; Palmieri, M.; Pasqualini, M.; Grifantini, M.; Costa, B.; Martini, C.; Franchetti, P. J Med Chem 2002, 45, 1196.
9. Torda, A. E.; Scheek, R. M.; Gunsteren, W. F. Chem Phys Lett 1989, 157, 289.
10. Pearlman, D. A.; Kollman, P. A. J Mol Biol 1991, 220, 457.
11. Torda, A. E.; Scheek, R. M.; van Gunsteren, W. F. J Mol Biol 1990, 214, 223.
12. Torda, A. E.; Brunne, R. M.; Huber, T.; Kessler, H.; van Gunsteren, W. F. J Biomol NMR 1993, 3, 55.
13. Pearlman, D. A. J Biomol NMR 1994, 4, 279.
14. Nanzer, A. P.; van Gunsteren, W. F.; Torda, A. E. J Biomol NMR 1995, 6, 313.
15. Plavec, J.; Koole, L. H.; Chattopadhyaya, J. Biochem Biophys Methods 1992, 25, 253.
16. Plavec, J.; Tong, W.; Chattopadhyaya, J. J Am Chem Soc 1993, 115, 9734.
17. Donders, L. A.; Deleeuw, F. A. A. M.; Altona, C. Magn Res Chem 1989, 27, 556.
18. Altona, C.; Ippel, J. H.; Hoekzema, A. J. A. W.; Erkelens, C.; Groesbeek, M.; Donders, L. A. Magn Res Chem 1989, 27, 564.
19. Altona, C.; Francke, R.; Dehaan, R.; Ippel, J. H.; Daalmans, G. J.; Hoekzema, A. J. A. W.; Vanwijk, J. Magn Res Chem 1994, 32, 670.
20. de Leeuw, H. P. M.; Haasnoot, C. A. G.; Altona, C. Isr J Chem 1980, 20, 108.
21. de Leeuw, F. A. A. M.; Altona, C. J Chem Soc Perkin Trans II 1982, 3, 375.
22. Diez, E.; Esteban, A. L.; Guilleme, J.; Bermejo, F. L. J Mol Struct 1981, 70, 61.
23. Diez, E.; Esteban, A. L.; Bermejo, F. L.; Altona, C.; de Leeuw, F. A. A. M. J Mol Struct 1984, 125, 49.
24. de Leeuw, F. A. A. M.; van Kampen P. N.; Altona, C.; Diez, E.; Esteban, A. L. J Mol Struct 1984, 125, 67.
25. Dzakula, Z.; DeRider, M. L.; Markley, J. L. J Am Chem Soc 1996, 118, 12796.
26. Dzakula, Z.; Westler, W. M.; Markley, J. L. J Magn Res 1996, 111, 109.
27. Hendrickx, P. M. S.; Martins, J. C. Chem Cent J 2008, 2, 20.
28. Van Wijk, J.; Huckriede, B. D.; Ippel, J. H.; Altona, C. Methods Enzymol 1992, 211, 286.
29. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, 2006.
30. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J Comput Chem 2000, 21, 132.
31. Jakalian, A.; Jack, D. B.; Bayly, C. I. J Comput Chem 2002, 23, 1623.
32. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
33. Corzana, F.; Busto, J. H.; Jiménez-Osés, G.; García de Luis, M.; Asensio, J. L.; Jiménez-Barbero, J.; Peregrina, J. M.; Avenoza, A. J Am Chem Soc 2007, 129, 9458.
34. Fernández-Tejada, A.; Corzana, F.; Busto, J. H.; Jiménez-Osés, G.; Peregrina, J. M.; Avenoza, A. Chem Eur J 2008, 14, 7042.
35. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J Comput Chem 2004, 25, 1157.
36. Wang, J.; Cieplak, P.; Kollman, P. A. J Comput Chem 2000, 21, 1049.