A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation

Journal of Physical Chemistry B

Volumn 111, Issue 13, 2007, Pages 3563-3569

  Cottone, Grazia ^a  

^a UNIVERSITY OF PALERMO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; MALTOSE; MOLECULAR DYNAMICS; MOLECULAR INTERACTIONS; SOLVENTS; WATER;

CARBOXY MYOGLOBIN; MOLECULAR DYNAMICS SIMULATION; PROTEIN DYNAMICS; PROTEIN STRUCTURE;

PROTEIN FOLDING;

EID: 34247518212     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0677288     Document Type: Article

References (60)

1. Hagen, S. J.; Hofrichter, J.; Eaton, W. A. Science 1995, 269, 959-962.
2. Gottfried, D. S.; Peterson, E. S.; Sheikh, A. G.; Wang, J.; Yang, M.; Friedman, J. M. J. Phys. Chem. 1996, 100, 12034-12042.
3. Kleinen, T.; Doster, W.; Leyser, H.; Petry, W.; Schwarz, V.; Settles, M. Biochemistry 1998, 37, 717-733.
4. Rector, D.; Jiang, J.; Berg, M. A.; Payer, M. D. J. Phys. Chem. B 2001, 105, 1081-1092.
5. Cordone, L.; Galajda, P.; Vitrano, E.; Gassmann, A.; Ostermann, A.; Parak, F. Eur. Biophys. J. 1998, 27, 173-176.
6. Cordone, L.; Ferrand, M.; Vitrano, E.; Zaccai, G. Biophys. J. 1999, 76, 1043-1047.
7. Librizzi, F.; Vitrano, E.; Cordone, L. Biophys. J. 1999, 76, 2727-2734.
8. Librizzi, F.; Paciaroni, A.; Pfister, C.; Vitrano, E.; Zaccai, G.; Cordone, L. In Proceedings of ILL Millenium Symposium and European User Meeting; ILL: Grenoble: France, 2001; pp 58-59.
9. Librizzi, F.; Viappiani, C.; Abbruzzetti, S.; Cordone, L. J. Chem. Phys. 2002, 116, 1193-1200.
10. Cottone, G.; Cordone, L.; Ciccotti, G. Biophys. J. 2001, 80, 931-938.
11. Cottone, G.; Ciccotti, G.; Cordone, L. J. Chem. Phys. 2002, 117, 9862-9866.
12. Belton, P. S.; Gil, A. M. Biopolymers 1994, 34, 957-961.
13. Cottone, G.; Giuffrida, S.; Ciccotti, G.; Cordone, L. Proteins: Struct., Funct., Bioinf. 2005, 59, 291-302.
14. Lins, R. D.; Pereira, C. S.; Hunenberger, P. H. Proteins: Struct., Funct., Bioinf. 2004, 55, 177-186.
15. Giuffrida, S.; Cottone, G.; Librizzi, F.; Cordone, L. J. Phys. Chem. B 2003, 107, 13211-13217.
16. Giuffrida, S.; Cottone, G.; Librizzi, F.; Cordone, L. In Progress in Condensed Matter Physics: Festschrift in Honour of Vincenzo Grosso; Mondio, G., Sipigni, L., Eds.; Italian Physical Society: Bologna, Italy, 2004; pp 131-138.
17. Giuffrida, S.; Cottone, G.; Cordone, L. J. Phys. Chem. B 2004, 108, 15415-15421.
18. Cordone, L.; Cottone, G.; Giuffrida, S.; Palazzo, G.; Venturoli, G.; Viappiani, C. Biochim. Biophys. Acta 2005, 1749, 252-281.
19. Giuffrida, S.; Cottone, G.; Cordone, L. Biophys. J. 2006, 91, 968-980.
20. Abbruzzetti, S.; Giuffrida, S.; Sottini, S.; Viappiani, C.; Cordone, L. Cell Biochim. Biophys. 2005, 42, 431-437.
21. Green, J. L.; Angell, C. A. J. Phys. Chem. 1989, 93, 2880-2882.
22. Melchionna, S.; Cozzini, S. DL-PROTEIN User Manual; http://www.sissa.it/om/DLPROTEIN. DL-PROTEIN has been developed from DL_POLY for the simulation of proteins by the Istituto Nazionale di Fisica della Materia, under the Network on "MD simulation of biosystems", group University of Rome La Sapienza. DL-POLY is a package of molecular simulation routines written by W. Smith and T. R. Forrester, copyright The Council for Central Laboratory of the Research Councils; Daresbury Laboratory at Daresbury: Nr. Warrington, U.K., 1996.
23. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
24. Ha, A. S. N.; Giammona, A.; Field, M.; Brady, J. W. Carbohydr. Res. 1988, 180, 207-221.
25. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 9, 26-935.
26. Cheng, X.; Schoenborn, B. P. Acta Crystallogr., Sect. B: Struct. Sci. 1990, 46, 195-208.
27. Gress, S. M. E.; Jeffrey, G. A. Acta Crystallogr., Sect. B: Struct. Sci. 1977, 33, 2490-2495.
28. Melchionna, S.; Ciccotti, G. J. Chem. Phys. 1997, 106, 195-199.
29. Allen M. P.; Tildesley D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
30. Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
31. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
32. Ciccotti, G.; Ryckaert, J. P. Comp. Phys. Rep. 1986, 4, 345-392.
33. Andersen, H. C. J. Comput. Phys. 1983, 52, 24-34.
34. Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 57, 1117-1157.
35. Kneller, G. R. Mol. Simul. 1991, 7, 113-119.
36. Maragliano, L.; Cottone, G.; Cordone, L.; Ciccotti, G. Biophys. J. 2004, 86, 2765-2772.
37. Luzar, A.; Chandler, D. Phys. Rev. Lett. 1996, 76, 928-930.
38. Lichtenegger, H.; Doster, W.; Kleinen, T.; Birk, A.; Sepiol, B.; Vogl, G. Biophys. J. 1999, 76, 414-422.
39. Vitkup, D.; Ringe, D.; Petsko, G. A.; Karplus, M. Nat. Struct. Biol. 2000, 7, 34-38.
40. Carpenter, J. F.; Crowe, J. H. Biochemistry 1989, 25, 3916-3922.
41. Sampedro, J. G.; Uribe, S. Mol. Cell Biochem. 2004, 250, 319-327.
42. Karen, E.; Tang, S.; Bloomfield, V. A. Biophys. J. 2002, 82, 2876-2891.
43. Rampp, M.; Buttersack, C.; Ludemann, H. D. Carbohydr. Res. 2000, 528, 561-572.
44. Roberts, C. J.; Debenedetti, P. G. J. Phys. Chem. B 1999, 103, 7308-7318.
45. Molinero, V.; Cagin, T.; Goddard, W. A., III. Chem. Phys Lett. 2003, 377, 469-474.
46. Lerbret, A.; Bordat, P.; Affouard, F.; Descamps, M.; Migliardo, F. J. Phys. Chem. B 2005, 109, 11046-11057.
47. Xie, G. F.; Timasheff, S. N. Biophys. Chem. 1997, 64, 25-43.
48. Massari, A. M.; Finkestein, I. J.; McClain, B. L.; Goj, A.; Wen, X.; Bren, K. L.; Loring, R. F.; Fayer, M. D. J. Am. Chem. Soc. 2005, 127, 14279-14289.
49. Lopez-Diez, E. C.; Bone, S. Phys. Med. Biol. 2000, 45, 3577-3588.
50. Allison, S. D.; Chang, B.; Randolph, T. W.; Carpenter, J. F. Arch. Biochem. Biophys. 1999, 365, 289-298.
51. Giachini, L.; Francia, F.; Cordone, L.; Boscherini, F.; Venturoli, G. Biophys. J. 2006, 92, 1350-1360.
52. Doster, W.; Bacheitner, A.; Dunau, R.; Hiebl, M.; Luscher, E. Biophys. J. 1986, 50, 213-219.
53. Tarek, M.; Tobias, D. J. Biophys. J. 2000, 79, 3244-3257.
54. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 8101-8104.
55. Magazù, S.; Maisano, G.; Migliardo, P.; Mondelli, C. Biophys. J. 2004, 86, 3241-3249.
56. Conrad, P. B.; de Pablo, J. J. J. Phys. Chem. A 1999, 103, 4049-4055.
57. Ekdawi-Sever, N. C.; Conrad, P. B.; de Pablo, J. J. J. Phys. Chem. A 2001, 105, 734-742.
58. Sakurai, M.; Murata, M.; Inoue, Y.; Hino, A.; Kobayashi, S. Bull. Chem. Soc. Jpn. 1997, 70, 847-858.
59. Massari, A. M.; Finkelstein, I. J.; Fayer, M. D. J. Am. Chem. Soc. 2006, 128, 3990-3997.
60. Timasheff, S. N. Annu. Rev. Biophys. Struct. 1993, 22, 67-97.