Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: A QM/MM metadynamics study

Journal of Physical Chemistry B

Volumn 113, Issue 20, 2009, Pages 7331-7339

  Petersen, Luis ^a   Ardèvol, Albert ^b   Rovira, Carme ^b,c   Reilly, Peter J ^a  

^a Iowa State University   (United States)

^b UNIVERSITY OF BARCELONA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BOATS; CELLULOSE; CHEMICAL BONDS; CRYSTAL STRUCTURE; ENZYME ACTIVITY; HYDROLYSIS; MOLECULAR MECHANICS; OXYGEN; SUGARS;

CARBON ATOMS; CATALYTIC MECHANISMS; CELLULOSE HYDROLYSIS; CLOSTRIDIUM THERMOCELLUM; DOUBLE BONDS; ENDOGLUCANASES; GENERAL BASE; GLUCANASE; GLUCOSYL RESIDUE; GLYCOSIDE HYDROLASE; GLYCOSIDIC BOND; HYDROLYZE CELLULOSE; LONE PAIR; METADYNAMICS; MICHAELIS COMPLEX; PROTON ACCEPTORS; REACTION COORDINATES; REACTION PATHWAYS; RING CONFORMATIONS; SEQUENCE HOMOLOGY; STRUCTURAL INFORMATION; STRUCTURAL SIMILARITY; TRANSITION STATE; XYLANASES;

DENSITY FUNCTIONAL THEORY;

BOATS; CELLULOSE; CHEMICAL BONDS; CRYSTAL STRUCTURE; ENZYMATIC ACTIVITY; HYDROLYSIS; OXYGEN; SUGARS;

EID: 67650045870     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp811470d     Document Type: Article

References (64)

1. Coutinho, P.; Henrissat, B. Carbohydrate-Active Enzymes Server 1999. http://www.cazy.org/.
2. Rye, C. S.; Withers, S. G. Curr. Opin. Chem. Biol. 2000, 4, 573-580.
3. Vasella, A.; Davies, G. J.; Bohm, M. Curr. Opin. Chem. Biol. 2002, 6, 619-629.
4. Vocadlo, D. J.; Davies, G. J. Curr. Opin. Chem. Biol. 2008, 12, 539-555.
5. Davies, G. J.; Ducros, V. M.; Varrot, A.; Zechel, D. L. Biocheim Soc. Trans. 2003, 31, 523-527.
6. Nerinckx, W.; Desmet, T.; Claeyssens, M. ARKIVOC 2006, xiii, 1-27.
7. Ducros, V. M.; Zechel, D. L.; Murshudov, G. N.; Gilbert, H. J.; Szabo, L.; Stoll, D.; Withers, S. G.; Davies, G. J. Angew. Chem. Int. Ed. 2002, 41, 2824-2827.
8. Biarnes, X.; Nieto, J.; Planas, A.; Rovira, C. J. Biol. Chem. 2006, 281, 1432-1441.
9. Mulakala, C.; Nerinckx, W.; Reilly, P. J. Carbohydr. Res. 2006, 341, 2233-2245.
10. Biarnes, X.; Ardevol, A.; Planas, A.; Rovira, C.; Laio, A.; Parrinello, M. J. Am. Soc. 2007, 129, 10686-10693.
11. Fushinobu, S.; Mertz, B.; Hill, A. D.; Hidaka, M.; Kitaoka, M.; Reilly, P. J. Carbohydr. Res. 2008, 343, 1023-1033.
12. Tailford, L. E.; Offen, W. A.; Smith, N. L.; Dumon, C.; Morland, C.; Gratien, J.; Heck, M. P.; Stick, R. V.; Bleriot, Y.; Vasella, A.; Gilbert, H. J.; Davies, G. J. Nat.Chem.Biol. 2008, 4, 306-312.
13. Greig, I. R.; Zahariev, F.; Withers, S. G. J. Am. Chem. Soc. 2008, 130, 17620-17628.
14. Soliman, M. E. S.; Ruggiero, G. D.; Ruiz Pernía, J. J.; Greig, I.; Williams, I. H. Org. Biomol. Chem. 2009, 7, 460-468.
15. Zechel, D. L.; Withers, S. G. Acc. Chem. Res. 2000, 33, 11-18.
16. Vocadlo, D. J.; Wicki, J.; Rupitz, K.; Withers, S. G. Biochemistry 2002, 41, 9727-9735.
17. Bottoni, A.; Miscione, G. P.; De Vivo, M. Proteins: Struct., Fund., Genet. 2005, 59, 118-130.
18. Bowman, A. L.; Grant, I. M.; Mulholland, A. J. Chem. Commun. (Cambridge. U.K.) 2008, 4425-4427.
19. Brás, N. F.; Moura-Tamames, S. A.; Fernandes, P. A.; Ramos, M. J. J. Comput. Chem. 2008, 29, 2565-2574.
20. Bayer, E. A.; Lamed, R.; Himmel, M. E. Curr. Opin. Biotechnol. 2007, 18, 237-245.
21. Himmel, M. E.; Ding, S. Y.; Johnson, D. K.; Adney, W. S.; Nimlos, M. R.; Brady, J. W.; Foust, T. D. Science 2007, 315, 804-807.
22. Sticklen, M. B. Nat. Rev. Genet. 2008, 9, 433-443.
23. Alzari, P. M.; Souchon, H.; Dominguez, R. Structure(Cambridge, MA, U.S.) 1996, 4, 265-275.
24. Koshland, D. E. Biol. Rev. Cambridge Philos. Soc. 1953, 28, 416-436.
25. Guerin, D. M.; Lascombe, M. B.; Costabel, M.; Souchon, H.; Lamzin, V.; Beguin, P.; Alzari, P. M. J. Mol. Biol. 2002, 316, 1061-1069.
26. Collins, T.; De Vos, D.; Hoyoux, A.; Savvides, S. N.; Gerday, C.; Van Beeumen, J.; Feller, G. J. Mol. Biol. 2005, 354, 425-435.
27. Yao, Q.; Sun, T.; Chen, G.; Liu, W. Biotechnol. Lett 2007, 29, 1243-1247.
28. Adachi, W.; Sakihama, Y.; Shimizu, S.; Fukazawa, T. S. T.; Suzuki, M.; Yatsunami, R.; Nakamura, S.; Takénaka, A. J. Mol. Biol. 2004, 343, 785-795.
29. Hightman, T. D.; Vasella, A. T. Angew. Chem., Int. Ed. 1999, 38, 750-770.
30. Sabini, E.; Sulzenbacher, G.; Dauter, M.; Dauter, Z.; Jorgensen, P. L.; Schülein, M.; Dupont, C.; Davies, G. J.; Wilson, K. S. Chem. Biol. 1999, 6, 483-492.
31. Pearlman, D. A.; Case, D. A.; Caldwell, J.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1-41.
32. Hornak, V.; Simmerling, C. Proteins: Struct., Funct., Genet. 2003, 51, 577-590.
33. Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; Gonzalez-Outeirino, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. J. Comput. Chem. 2008, 29, 622-655.
34. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem.Phys. 1983, 79, 926-935.
35. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38.
36. Laio, A.; VandeVondele, J.; Rothlisberger, U. J. Chem. Phys. 2002, 116, 6941-6947.
37. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
38. Von Lilienfeld, O. A.; Tavernelli, I.; Rothlisberger, U. J. Chem. Phys. 2005, 122, 014113.
39. Hünenberger, P. J. Chem. Phys. 2000, 113, 10464-10476.
40. Carloni, P.; Rothlisberger, U.; Parrinello, M. Acc. Chem. Res. 2002, 35, 455-464.
41. Dal Peraro, M.; Ruggerone, P.; Raugei, S.; Gervasio, F. L.; Carloni, P. Curr. Opin. Struct. Biol. 2007, 17, 149-156.
42. Troullier, N.; Martins, J. L. Phys. Rev. Condens. MatterMater. Phys. 1991, 43, 1993-2006.
43. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868.
44. Ireta, J.; Neugebauer, J.; Scheffler, M. J. Phys. Chem. A 2004, 108, 5692-5698.
45. Nosé, S. J. Chem. Phys. 1984, 81, 511-519.
46. Marzari, N.; Vanderbilt, D. Phys. Rev. B. Condens. MatterMater. Phys. 1997, 56, 12847-12865.
47. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302.
48. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566.
49. Ensing, B.; Laio, A.; Parrinello, M.; Klein, M. L. J. Phys. Chem. B 2005, 109, 6676-6687.
50. Oganov, A. R.; Martonak, R.; Laio, A.; Raiteri, P.; Parrinello, M. Nature (London) 2005, 438, 1142-1144.
51. Blumberger, J.; Ensing, B.; Klein, M. L. Angew. Chem. Int. Ed. 2006, 45, 2893-2897.
52. Fiorin, G.; Pastore, A.; Carloni, P.; Parrinello, M. Biophys. J. 2006, 91, 2768-2777.
53. Martonak, R.; Donadio, D.; Oganov, A. R.; Parrinello, M. Nat. Mater. 2006, 5, 623-626.
54. Rodriguez-Fortea, A.; Iannuzzi, M.; Parrinello, M. J. Phys. Chem. B 2006, 110, 3477-3484.
55. Guthrie, R. D.; Jencks, W. P. Acc. Chem. Res. 1989, 22, 344-349.
56. Guthrie, R. D. Pure Appl. Chem. 1989, 61, 23-56.
57. Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737-7744.
58. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
59. Sinnott, M. Biochem. J. 1984, 224, 817-821.
60. Deslongchamps, P. Pure Appl.Chem. 1993, 65, 1161-1178.
61. Cremer, D.; Pople, J. A. J. Am. Chem. Soc. 1975, 97, 1354-1358.
62. Vocadlo, D. J.; Davies, G. J.; Laine, R.; Withers, S. G. Nature (London) 2001, 412, 835-838.
63. Schramm, V. L.; Shi, W. Curr. Opin. Struct. Biol. 2001, 11, 657-665.
64. Watts, A. G.; Damager, I.; Amaya, M. L.; Buschiazzo, A.; Alzari, P.; Frasch, A. C.; Withers, S. G. J. Am. Chem. Soc. 2003, 125, 7532-7533.