Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates

Journal of Computational Chemistry

Volumn 29, Issue 15, 2008, Pages 2565-2574

  Brás, Natércia F ^a   Moura Tamames, Sara A ^a   Fernandes, Pedro A ^a   Ramos, Maria J ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

Charge distribution; Glycoside hydrolysis; Oxocarbenium ion character; Retaining mechanism; Transition state

Indexed keywords

ABS RESINS; ATOMIC PHYSICS; ATOMS; BRIDGES; COMPUTATIONAL METHODS; DISSOCIATION; ENZYMES; GLUCOSE; HYDROGEN; OXYGEN; SUGAR (SUCROSE); SULFUR COMPOUNDS;

ACTIVATION BARRIERS; ANOMERIC CARBONS; ATOMIC CHARGES; DFT CALCULATIONS; DISSOCIATIVE CHARACTERS; DISSOCIATIVE MECHANISMS; DOUBLE BONDS; GLYCOSIDASE; GLYCOSIDE HYDROLASES; GLYCOSIDE HYDROLYSIS; GLYCOSIDIC BONDS; HYDROGEN BRIDGES; INHIBITORY EFFECTS; MECHANISTIC STUDIES; MULTIPLE CELLULAR PROCESSES; OH GROUPS; OXOCARBENIUM ION CHARACTER; POSITIVE CHARGES; REACTION CENTERS; REACTION MECHANISMS; RETAINING MECHANISM; RING DISTORTIONS; SUGAR RINGS; TRANSITION STATE; TRANSITION STATES;

SUGARS;

GLYCOSIDASE; GLYCOSIDE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; ENZYME ACTIVATION; ENZYME ACTIVE SITE; HYDROLYSIS; METABOLISM; THERMODYNAMICS;

CATALYTIC DOMAIN; ENZYME ACTIVATION; GLYCOSIDE HYDROLASES; GLYCOSIDES; HYDROLYSIS; MODELS, CHEMICAL; MODELS, MOLECULAR; THERMODYNAMICS;

EID: 55349124348     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21013     Document Type: Article

References (49)

1. Zechel, D. L.; Withers, S. G. Acc Chem Res 2000, 33, 11.
2. Wolfenden, R.; Lu, X.; Young, G. J Am Chem Soc 1998, 120, 6814.
3. Dwek, R. A. Chem Rev 1996, 96, 683.
4. Sears, P.; Wong, C. H. Proc Natl Acad Sci USA 1996, 93, 12086.
5. Cutfield, S. M.; Davies, G. J.; Murshudov, G.; Anderson, B. F.; Moody, P. C. E.; Sullivan, P. A.; Cutfield, J. F. J Mol Biol 1999, 294, 771.
6. Henrissat, B.; Davies, G. Curr Opin Struct Biol 1997, 7, 637.
7. Kempton, J. B.; Withers, S. G. Biochemistry 1992, 31, 9961.
8. NamChuk, M. N.; McCarter, J. D.; Becalski, A.; Andrews, T.; Withers, S. G. J Am Chem Soc 2000, 122, 1270.
9. Namchuk, M. N.; Wither, S. G. Biochemistry 1995, 34, 16194.
10. Cerqueira, N. M. F. S. A.; Femandes, P. A.; Eriksson, L. A.; Ramos, M. J. Biophys J 2006, 90, 2109.
11. Botonni, A.; Miscine, G. P.; de Vivo, M. Proteins: Struct Funct Bioinformatics 2005, 59, 118.
12. Levitt, M.; Warshel, A. J Mol Biol 1976, 103, 227.
13. Juers, D. H.; Heightman, T. D.; Vasella, A.; MacCarter, J. D.; Mackenzie, L.; Withers, S. G.; Matthews, B. W. Biochemistry 2001, 40, 14781.
14. Barone, V.; Cossi, M. J Phys Chem A 1998, 102, 1995.
15. Carpenter, J. E.; Weinhold, F. J Mol Struct: Theochem 1988, 169, 41.
16. Foster, J. P.; Weinhold, F. J Am Chem Soc 1980, 102, 7211.
17. Reed, A. E.; Weinhold, F. J Chem Phys 1983, 78, 4066.
18. Reed, A. E.; Weinhold, F. J Chem Phys 1985, 83, 1736.
19. Reed, A. E.; Weinstock, R. B.; Weinhold, F. J Chem Phys 1985, 83, 735.
20. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem Rev 1988, 88, 899.
21. Weinhold, F.; Carpenter, J. E. The Structure of Small Molecules and Ions, Naaman, R.; Vager, Z., Eds.; Plenum, New York, 1998, pp. 227-236.
22. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Tyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.: Bakken. V.; Adamo, C.; Jaramillo, J.; Gomperts, R.: Stratmann. R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari. K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, 1; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision B, 04 ed.; Gaussian Inc.: Pittsburgh PA, 2003.
23. Himo, F.; Siegbahn, P. E. M. Chem Rev 2003, 103, 2421.
24. Becke, A. D. J Chem Phys 1996, 104, 1040.
25. Lee, C.; Yang, W.; Parr, R. G. Phys Rev B 1988, 37, 785.
26. Becke, A. D. Phys Rev A 1988, 38, 3098.
27. Russo, N.; Marino, T.; Toscano, M.; Grand, A.; Leopoldini, M. J Inorg Biochem 2003, 96, 221.
28. Hamprecht, F. A.; Cohen, A. J.; Handy, N. C. J Chem Phys 1998, 109, 6264.
29. Schmider, H. L.; Becke, A. D. J Chem Phys 1998, 108, 9624.
30. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys Rev Lett 1996, 77, 3865.
31. Zhao, Y.; Lynnch, B. J.; Truhlar, D. G. J Phys Chem A 2004, 108, 2715.
32. Adamo, C.; Barone, V. J Chem Phys 1998, 108, 664.
33. Perdew, J. P. Unified Theory of Exchange and Correlation Beyond the Local Density Approximation. In Electronic Structure of Solids '91; Ziesche, P.; Eschig, H., Eds.; Akademie Verlag: Berlin, Germany, 1991; pp. 11-20.
34. Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D.G. J Phys Chem A 2000, 104, 4811.
35. Lynch, B. J.; Zhao, Y.; Truhlar, D. G. J Phys Chem A 2003, 107, 1384.
36. Zhao, Y.; Truhlar, D. G. J Phys Chem A 2004, 108, 6908.
37. Sousa, S. S.; Fernandes, A. P.; Ramos, M. J. J Phys Chem A 2007, 111, 10439.
38. Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem Phys Lett 1988, 153, 503.
39. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem Phys Lett 1990, 166, 275.
40. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem Phys Lett 1990, 166, 281.
41. Head-Gordon, M.; Head-Gordon, T. Chem Phys Lett 1994, 220, 122.
42. Saebo, S.; Almlof, J. Chem Phys Lett 1989, 154, 83.
43. Pople, J. A.; Head-Gordon, M.; Raghavachari, K. J Chem Phys 1987, 87, 5968.
44. McCarter, J.; Withers, S. G. Curr Opin Struct Biol 1994, 4, 885.
45. Dinner, A. R.; Blackburn, G. M.; Karplus, M. Nature 2001, 413, 752.
46. Vocadlo, D. J.; Davies, G. J.; Laine, R.; Withers, S. G. Nature 2001, 412, 835.
47. Andrews, C. W.; Fraser-Reid, B.; Bowen, J. P. J Am Chem Soc 1991, 113, 8293.
48. Himo, F. Theor Chem Acc 2006, 116, 232.
49. Vasella, A.; Davies, G. J.; Bohm, M. Curr Opin Chem Biol 2002, 6, 619.