Transition path sampling study of the reaction catalyzed by purine nucleoside phosphorylase

Zeitschrift fur Physikalische Chemie

Volumn 222, Issue 8-9, 2008, Pages 1359-1374

  Saen oon, Suwipa ^a   Schramm, Vern L ^a   Schwartz, Steven D ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Enzyme catalyzes; Purine nucleoside phosphorylase; Transition path sampling

Indexed keywords

CATALYSIS; ENZYMES; MOLECULAR MODELING; PHOSPHORYLATION; QUANTUM THEORY;

CONFORMATIONAL CHANGE; PURINE NUCLEOSIDE PHOSPHORYLASE; QUANTUM MECHANICAL/MOLECULAR MECHANICAL; REACTION COORDINATES; REACTIVE TRAJECTORIES; SIGNIFICANT VARIABLES; TRANSITION PATH SAMPLING; TRANSITION STATE STRUCTURE;

BIOMOLECULES;

EID: 57349195110     PISSN: 09429352     EISSN: None     Source Type: Journal    
DOI: 10.1524/zpch.2008.5395     Document Type: Article

References (31)

1. J. D. Stoeckler, C. Cambor, and R. E. J. Parks, Biochemistry 19 (1980) 102.
2. E. R. Giblett, A. J. Ammann, D. W. Wara, R. Sandman, and L. K. Diamond, Lancet 1 (1975) 1010.
3. S. E. Ealick, Y. Babu, C. Bugg, M. E. Erion, W. C. Guida, J. A. Montgomery, and J. A. Secrist, Proc. Natl. Acad. Sci. USA 88 (1991) 11540.
4. V. L. Schramm and W. Shi, Curr. Opin. Chem. Biol. 11 (2001) 657.
5. C. Dellago, P. Bolhuis, and P. Geissler, Adv. Chem. Phys. 123 (2001) 1.
6. C. Dellago and P. Bolhuis, Top. Curr. Chem. 268 (2007) 291.
7. J. E. Basner and S. D. Schwartz, J. Am. Chem. Soc. 127 (2005) 13822.
8. S. L. Quaytman and S. D. Schwartz, Proc. Natl. Acad. Sci. USA 104 (2007) 12253.
9. M. Field, P. Bash, and M. Karplus, J. Comp. Chem. 11 (1990) 700.
10. W. Shi, L. M. Ting, G. A. Kicsha, A. Lewandowicz, P. L. Tyler, R. H. Furneaux, S. C. Almo, and V. L. Schramm, J. Biol. Chem. 279 (2004) 18103.
11. P. C. Kline and V. L. Schramm, Biochemistry 32 (1993) 13212.
12. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4 (1983) 187.
13. J. J. P. Stewart, J. Comp. Chem. 10 (1989) 209.
14. J. C. Hart, N. A. Burton, I. H. Hillier, M. J. Harrison, and P. Jewsbury, Chem. Commun. (1997) 1431.
15. P. G. Bolhuis, Proc. Natl. Acad. Sci. USA 100 (2003) 12129.
16. G. M. V. J. P. Torrie, J. Comput. Phys. 23 (1977) 187.
17. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13 (1992) 1011.
18. H. N. Chen, B. Ilan, Y. J. Wu, F. Q. Zhu, K. Schulten, and G. A. Voth, Biophys. J. 92 (2007) 46.
19. G. Hummer, J. Chem. Phys. 114 (2001) 7330.
20. S. Park, F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten, J. Chem. Phys. 119 (2003) 3559.
21. M. Ghanem, L. Li, C. Wing, and V. L. Schramm, Biochemistry 47 (2008) 2559.
22. P. Bolhuis, C. Dellago, and D. Chandler, Faraday Discuss. 110 (1998) 421.
23. S. Saen-oon, V. L. Schramm, and S. D. Schwartz, submitted to Proc. Natl. Acad. Sci. USA (2008).
24. S. Nunez, D. Antoniou, V. L. Schramm, and S. D. Schwartz, J. Am. Chem. Soc. 126 (2004) 15720.
25. S. Saen-oon, M. Ghanem, V. L. Schramm, and S. D. Schwartz, Biophys. J. (2008) in press.
26. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Milla, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ay- ala, Q. Cui, K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople. Gaussian 98, Revision A.11.2 (Gaussian, Inc., Pittsburgh, 2001).
27. D. Antoniou, J. Basner, S.Nunez, and S. D. Schwartz, Chem. Rev. 106 (2006) 3170.
28. D. T. Major and J. Gao, J. Am. Chem. Soc. 126 (2006) 16345.
29. J. C. Hermann, C. Hensen, L. Ridder, A. J. Mulholland, and H.-D. Holtje, J. Am. Chem. Soc. 127 (2005) 4454.
30. M. D. Erion, K. Takabayashi, H. Smith, J. Kessi, S. Wagner, S. Honger, S. Shames, and S. E. Ealick, Biochemistry 36 (1997) 11725.
31. A. S. Murkin, M. R. Birck, A. Rinaldo-Matthis, W. Shi, E. A. Taylor, and V. L. Schramm, Biochemistry 46 (2007) 5038.