pK a analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications

Journal of Physical Chemistry A

Volumn 111, Issue 26, 2007, Pages 5703-5711

  Riccardi, Demian ^a   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONIC ANHYDRASE; GENERALIZED SOLVENT BOUNDARY POTENTIAL (GSBP); INTERCONVERSION;

BIOMOLECULES; BOUNDARY CONDITIONS; COMPUTER SIMULATION; ENZYMES; QUANTUM THEORY; REACTION KINETICS; ZINC;

WATER;

CARBONATE DEHYDRATASE II; GLUTAMIC ACID; WATER; ZINC;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; GENETICS; HUMAN; METABOLISM; MUTATION; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CARBONIC ANHYDRASE II; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; GLUTAMIC ACID; HUMANS; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS; WATER; ZINC;

EID: 34547480925     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp070699w     Document Type: Conference Paper

References (56)

1. Tu, C.; Tripp, B. C.; Ferry, J. G.; Silverman, D. N. J. Am. Chem. Soc. 2001, 123, 5861.
2. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227.
3. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700.
4. Lipkowitz, K. B., Boyd, D. B., Eds. Gao, J. In Reviews in Computational Chemistry VII; VCH: New York, 1995.
5. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467.
6. Shurki, A.; Warshel, A. Adv. Prot. Chem. 2003, 66, 249.
7. Friesner, R. A.; Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389.
8. Shaik, S.; Kumar, D.; de Visser, S. P.; Altun, A.; Thiel, W. Chem. Rev. 2005, 105, 2279.
9. Merz, J. K. M. Curr. Opin. Struct. Biol. 1993, 3, 234.
10. Zhang, Y. K.; Liu, H. Y.; Yang, W. T. J. Chem. Phys. 2000, 112, 3483.
11. Cui, Q.; Karplus, M. Adv. Prot. Chem. 2003, 66, 315.
12. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; Konig, P.; Li, G.; Xu, D.; Guo, H.; et al. J. Phys. Chem. B 2006, 110, 6458.
13. Cui, Q. Theor. Chem. Acc. 2006, 116, 51.
14. Im, W.; Bernéche, S.; Roux, B. J. Chem. Phys. 2001, 114, 2924.
15. Schaefer, P.; Riccardi, D.; Cui, Q. J. Chem. Phys. 2005, 123, 014905.
16. Gregersen, B. A.; York, D. M. J. Phys. Chem. B 2005, 109, 536.
17. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solution; Wiley: New York, 1991.
18. Brooks, C. L., III; Karplus, M. J. Mol. Biol. 1989, 208, 159.
19. Koenig, P.; Ghosh, N.; Hoffman, M.; Elstner, M.; Tajkhorshid, E.; Frauenheim, T.; Cui, Q. J. Phys. Chem. A 2006, 110, 548 (Donald G. Truhlar Festschrift).
20. Riccardi, D.; Schaefer, P.; Cui, Q. J. Phys. Chem. B 2005, 109, 17715.
21. Riccardi, D.; König, P.; Prat-Resina, X.; Yu, H.; Elstner, M.; Frauenheim, T.; Cui, Q. J. Am. Chem. Soc. 2006, 128, 16302.
22. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30.
23. Silverman, D. N. Methods Enzymol. 1995, 249, 479.
24. Silverman, D. N. Biochim. Biophys. Acta. 2000, 1458, 88.
25. Warshel, A. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425.
26. Silverman, D. N.; Tu, C. K. J. Am. Chem. Soc. 1975, 97, 2263.
27. Toba, S.; Colombo, G.; Merz, K. M. J. J. Am. Chem. Soc. 1999, 121, 2290.
28. Elstner, M.; Porezag, D.; Jungnickel, G.; Elstner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 1160.
29. Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Phys. Chem. B 2001, 105, 569.
30. Elstner, M.; Cui, Q.; Munih, P.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Comput. Chem. 2003, 24, 565.
31. Elstner, M.; Frauenheim, T.; Suhai, S. THEOCHEM 2003, 632, 29.
32. Elstner, M. Theo. Chem. Acc. 2006, 116, 316.
33. MacKerell, A. D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R. L.; Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; et al. J. Phys. Chem. B 1998, 102, 3586.
34. Antes, I.; Thiel, W. J. Phys. Chem. A 1999, 103, 9290.
35. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720.
36. Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chattfield, D. C.; Hodošček, M.; Brooks, B. R. J. Chem. Phys. 2002, 117, 10534.
37. Konig, P. H.; Hoffmann, M.; Frauenheim, T.; Cui, Q. J. Phys. Chem. B 2005, 109, 9082.
38. Riccardi, D.; Li, G.; Cui, Q. J. Phys. Chem. B 2004, 108, 6467.
39. Hâkansson, K.; Carlsson, M.; Svensson, L. A.; Liljas, A. J. Mol. Biol. 1992, 227, 1192.
40. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
41. Nina, M.; Roux, B. J. Phys. Chem. B 1997, 101, 5239.
42. Rychaert, J. P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327.
43. Li, G.; Zhang, X.; Cui, Q. J. Phys. Chem. B 2003, 107, 8643.
44. Li, G.; Cui, Q. J. Phys. Chem. B 2003, 107, 14521.
45. Liang, Z.; Xue, Y.; Behravan, G.; Jonsson, B.; Lindskog, S. Eur. J. Biochem. 1993, 211, 821.
46. Xue, Y.; Liljas, A.; Jonsson, B.; Lindskog, S. Proteins: Struct. Funct. Genet. 1993, 17, 93.
47. Lide, D. R., Ed. CRC Handbook Chemistry and Physics, 85th ed; CRC Press: Boca Raton, FL, 2005.
48. Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167.
49. Yang, W.; Bitetti-Putzer, R.; Karplus, M. J. Chem. Phys. 2004, 120, 2618.
50. Roux, B.; Yu, H.; Karplus, M. J. Phys. Chem. 1990, 94, 4683.
51. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196.
52. Boehr, D. D.; Dyson, H. J.; Wright, P. E. Chem. Rev. 2006, 106, 3055.
53. Kovrigin, E. L.; Loria, J. P. Biochemistry 2006, 45, 2636.
54. Olsson, M. H. M.; Parson, W. W.; Warshel, A. Chem. Rev. 2006, 106, 1737.
55. Haywards, S.; Go, N. Annu. Rev. Phys. Chem. 1995, 46, 223.
56. Kato, M.; Pisliakov, A. V.; Warshel, A. Proteins: Struct. Funct. Bioinform. 2006, 64, 829.