Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of Cp NagJ in complex with PUGNAc

Journal of Physical Chemistry B

Volumn 114, Issue 20, 2010, Pages 7029-7036

  Lameira, Jeronimo ^a,b   Alves, Cláudio Nahum ^a   Moliner, Vicent ^b,c   Martí, Sergio ^b   Castillo, Raquel ^b   Tuñón, Iñaki ^d  

^a FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^b UNIVERSITAT JAUME I   (Spain)

^c LODZ UNIVERSITY OF TECHNOLOGY   (Poland)

^d UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; ELECTROSTATICS; ENZYMES; FREE ENERGY; MOLECULAR DYNAMICS; REACTION KINETICS;

ACETAMIDO; ASPARTATE RESIDUE; CLOSTRIDIUM PERFRINGENS; D-GLUCOPYRANOSE; ELECTROSTATIC BINDING; EXPERIMENTAL DATA; MODIFIED PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; N-ACETYLGLUCOSAMINE; QUANTUM MECHANICAL/MOLECULAR MECHANICAL; REACTION MECHANISM; STRONG INTERACTION; SUBSTRATE BINDING; THEORETICAL PREDICTION; THEORETICAL RESULT; WILD TYPES;

BINDING ENERGY;

EID: 77952707954     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9115673     Document Type: Article

References (34)

1. Torres, C. R.; Hart, G. W. J. Biol. Chem. 1984, 259, 3308-3317
2. Wells, L.; Vosseller, K.; Hart, G. W. Science 2001, 291, 2376-2378
3. Hanover, J. A. FASEB J. 2001, 15, 1865-1876
4. Dong, D. L.; Xu, Z. S.; Hart, G. W.; Cleveland, D. W. J. Biol. Chem. 1996, 271, 20845-20852
5. Arnold, C. S.; Johnson, G. V.; Cole, R. N.; Dong, D.; Lee, M.; Hart, G. W. J. Biol. Chem. 1996, 271, 28741-28744
6. Shafi, R.; Iyer, S. P. N. L.; Ellies, G.; O'Donnell, N.; Marek, K. W.; Chui, D.; Hart, G. W.; Marth, J. D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5735-5739
7. Park, S. Y.; Ryu, J. W.; Lee, W. Exp. Mol. Med. 2005, 37, 220-229
8. Rao, F. V.; Dorfmueller, H. C.; Villa, F.; Allwood, M.; Eggleston, I.; van Aalten, D. M. EMBO J. 2006, 25, 1569-1578
9. Whitworth, G. E.; Macauley, M. S.; Stubbs, K. A.; Dennis, R. J.; Taylor, E. J.; Davies, G. J.; Greig, I. R.; Vocadlo, D. J. J. Am. Chem. Soc. 2007, 129, 635-644
10. Lameira, J.; Alves, C. N.; Kanaan, N.; Moliner, V.; Tuñón, I.; Martí, S. J. Phys. Chem. B 2008, 112, 14260-14266
11. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249
12. Alves, C. N.; Martí, S.; Castillo, R.; Andrés, J.; Moliner, V.; Tuñón, I.; Silla, E. Chem.-Eur. J. 2007, 13, 7715-7724
13. Gao, J.; Xia, X. Science 1992, 258, 631-635
14. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415-436
15. Field, M.; David, L.; Rinaldo, D. Personal Communication.
16. Cisetinbas, N.; Macauley, M. S.; Stubbs, K. A.; Drapala, R.; Vocadlo, D. J. Biochemistry 2006, 45, 3835-3844
17. Byrd, R. H.; Lu, P. H.; Nocedal, J.; Zhu, C. Y. SIAM J. Sci. Comput. 1995, 16, 1190-1208
18. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1986, 7, 718-730
19. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733
20. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909
21. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
22. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
23. Field, M. J. A practical Introduction to the Simulation of Molecular Systems; Cambridge University Press: Cambridge, U.K., 1999.
24. Field, M. J.; Albe, M.; Bret, C.; Proust-de Martin, F.; Thomas, A J. Comput. Chem. 2000, 21, 1088-1100
25. Zhang, Y.; Liu, H.; Yang, W. J. Chem. Phys. 2000, 112, 3483-3492
26. Martí, S.; Moliner, V.; Tuñón, I. J. Chem. Theory Comput. 2005, 1, 1008-1016
27. Breneman, C. M.; Wiberg, K. B. J. Comput. Chem. 1990, 11, 361-373
28. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313
29. McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976; p 266.
30. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282
31. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
32. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199
33. Warshel, A.; Sharma, P. K.; Chu, Z. T.; Åqvist, J. Biochemistry 2007, 46, 1466-1476
34. Kraut, D. A.; Sigala, P. A.; Pybus, B.; Liu, C. W.; Ringe, D.; Petsko, G. A.; Herschlag, D. PLoS Biol. 2006, 4 0501-0519