Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: Application to lipoxygenase

Journal of Physical Chemistry B

Volumn 112, Issue 19, 2008, Pages 5950-5954

  Mavri, Janez ^a,b   Liu, Hanbin ^b   Olsson, Mats H M ^b   Warshel, Arien ^b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; CARRIER MOBILITY; CRACK PROPAGATION; DEUTERIUM; DYNAMICS; ENZYMES; FREE ENERGY; FUNCTIONS; HYDROGEN; ISOTOPES; MOLECULAR DYNAMICS; PROTEINS; QUANTUM CHEMISTRY; WAVE FUNCTIONS;

ACTIVATION BARRIERS; ACTIVATION FREE ENERGIES; CLASSICAL-QUANTUM; DYNAMICAL EFFECTS; ENZYME CATALYSIS; FREE ENERGY CHANGE; ISOTOPE EFFECTS; KINETIC ISOTOPE EFFECT; LIPOXYGENASE; LONG TIME; MOLECULAR DYNAMICS SIMULATION; NUCLEAR WAVE FUNCTIONS; PATH METHOD; PROTON POTENTIALS; QUANTUM-CLASSICAL; QUANTUM-MECHANICAL; REACTING SYSTEMS; SOYBEAN LIPOXYGENASE; VALENCE BOND;

RATE CONSTANTS;

HYDROGEN; LIPOXYGENASE; LIPOXYGENASE L 1; LIPOXYGENASE L-1;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; METABOLISM; QUANTUM THEORY; SOYBEAN; SURFACE PROPERTY;

CATALYSIS; COMPUTER SIMULATION; HYDROGEN; LIPOXYGENASE; MOLECULAR STRUCTURE; QUANTUM THEORY; SOYBEANS; SURFACE PROPERTIES;

EID: 44949221121     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0758420     Document Type: Article

References (41)

1. Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H.; Olsson, M. H. M. Chem. Rev. 2006, 106, 3210.
2. Olsson, M. H. M.; Parson, W. W.; Warshel, A. Chem. Rev. 2006, 106, 1737.
3. Held, M. J. J. Comput. Chem. 2002, 23, 48.
4. Mulholland, A. J.; Grant, G. H.; Richards, W. G. Protein Eng. 1993, 6, 133.
5. Koben, A.; Klinman, J. P. J. Am Chem. Soc. 2000, 122, 10738.
6. Nunez, S.; Antoniou, D.; Schramm, V. L.; Schwartz, S. D. J. Am. Chem. Soc. 2004, 126, 15720.
7. Scrutton, N. S.; Basran, J.; Sutcliffe, M. J. Eur. J. Biochem 1999, 264, 666.
8. Knapp, M. J.; Rickert, K.; Klinman, J. P. J. Am. Chem. Soc. 2002, 124, 3865.
9. Ball, P. Nature 2004, 431, 396.
10. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions, 1997 ed.; John Wiley & Sons: New York, 1991.
11. Olsson, M. H. M.; Siegbahn, P. E. M.; Warshel, A. J. Am Chem. Soc. 2004, 126, 2820.
12. Olsson, M. H. M.; Mavri, J.; Warshel, A. Philos. Trans. R. Soc. London, Ser. B 2006, 361, 1417.
13. Hwang, J.-K.; Warshel, A. J. Am. Chem. Soc. 1996, 118, 11745.
14. Hwang, J.-K.; Warshel, A. J. Phys. Chem. 1993, 97, 10053.
15. Hwang, J.-K.; Chu, Z. T.; Yadav, A.; Warshel, A. J. Phys. Chem. 1991, 95, 8445.
16. Wang, M. L.; Lu, Z. Y.; Yang, W. T. J. Chem. Phys. 2006, 124, 1 124516.
17. Wang, Q.; Hammes-Schiffer, S. J. Chem. Phys. 2006, 125, 184102.
18. Major, D. T.; Gao, J. L. J. Mol. Graphics 2005, 24, 121.
19. Gao, J. L.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467.
20. Billeter, S. R.; Webb, S. P.; Agarwal, P. K.; Iordanov, T.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2081, 123, 11262.
21. Kuznetsov, A. M.; Ulstrap, J. Can. Chem. J. 1999, 77, 1085.
22. Yamamoto, T.; Miller, W. H. J. Chem. Phys. 2005, 122.
23. Kosloff, D.; Kosloff, R. J. Comput. Phys. 1983, 52, 35.
24. Hatcher, E.; Soudackov, A. V.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2004, 126, 5763.
25. Tejero, I.; Garcia-Viloca, M.; Gonzalez-Lafont, A.; Lluch, J. M.; York, D. M. J. Phys. Chem. B 2006, 110, 24708.
26. Hatcher, E.; Soudackov, A. V.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2007, 129, 187.
27. Lee, F. S.; Chu, Z. T.; Warshel, A. J. Comput. Chem. 1993, 14, 161.
28. Chu, Z. T.; Villa, J.; Strajbl, M.; Schutz, C.; Shurki, A.; Warshel, A. Molaris, 9.05, b; Los Angeles, 2002.
29. Aqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523.
30. King, G.; Warshel, A. J. Chem. Phys. 1989, 91, 3647.
31. Lee, F. S.; Warshel, A. J. Chem. Phys. 1992, 97, 3100.
32. Villa, J.; Warshel, A. J. Phys. Chem. B 2001, 105, 7887.
33. Berendsen, H. J. C.; Mavri, J. J. Phys. Chem. 1993, 97, 13464.
34. Billeter, S. R.; van Gunsteren, W. F. Mol. Simul. 1995, 15, 301.
35. Iyengar, S. S.; Jakowski, J. J. Chem. Phys. 2005, 122.
36. Lensink, M. F.; Mavri, J.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 886.
37. Gillan, M. J. J. Phys. C. Solid State Phys. 1987, 20, 3621.
38. Voth, G. A.; Chandler, D.; Miller, W. H. J. Chem. Phys. 1989, 91, 7749.
39. Warshel, A.; Parson, W. W. Q. Rev. Biophys. 2001, 34, 563.
40. Liu, H. B.; Warshel, A. J. Phys. Chem. B 2067, 111, 7852.
41. Feierberg, I.; Luzhkov, V.; Aqvist, J. J. Biol. Chem. 2000, 275, 22657.